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So far, the only experimental structural information on the nAChRs came
from electron microscopy studies on Torpedo receptors^[55]18, ^[56]19,
^[57]20. These lowâmedium-resolution studies revealed the overall shape
and dimensions of the receptor, a location of the ligand-binding site
and the organization of the ion channel. The most recent 4.6 Ã
data^[58]21 showed acetylcholine-binding pockets surrounded by
seven-stranded beta -sheet structures. This fits with circular
dichroism measurements demonstrating that LBDs are predominantly beta
-structured^[59]22, ^[60]23, ^[61]24. No high-resolution data are
available yet and although soluble LBDs have been produced^[62]22,
^[63]23, ^[64]24, ^[65]25, ^[66]26, protein quantities were
insufficient for high-resolution studies.
[67]Top of page
§3§ Acetylcholine-binding protein §3§
Acetylcholine-binding protein (AChBP) is a soluble protein found in the
snail Lymnaea stagnalis^[68]27. It is produced and stored in glial
cells, and released in an acetylcholine-dependent manner into the
synaptic cleft, where it modulates synaptic transmission. Mature AChBP
is 210 residues long and forms a stable homopentamer. It aligns with
the N-terminal domains of pentameric LGICs ([69]Fig. 1) and lacks the
transmembrane and intracellular domains present in the
superfamily^[70]27. AChBP is most closely related to the alpha
-subunits of the nAChRs ([71]Fig. 1). Nearly all residues that are
conserved within the nAChR family are present in AChBP, including those
that are relevant for ligand binding. Moreover, AChBP binds known nAChR
agonists and competitive antagonists such as acetylcholine, nicotine,
d-tubocurarine and alpha -bungarotoxin^[72]27. Therefore, AChBP can be
used as an example of the N-terminal domain of an alpha -subunit
of nAChRs. Here we report the crystal structure of the AChBP
homopentamer at 2.7 Ã
resolution.
§5§ [73] Figure 1: Sequence alignment of AChBP with pentameric ligand-gated
ion channels (LGICs). §5§
[74]Figure 1 : Sequence alignment of AChBP with pentameric ligand-gated
ion channels (LGICs). Unfortunately we are unable to provide accessible
alternative text for this. If you require assistance to access this
image, or to obtain a text description, please contact npg@nature.com
The alignment shows only the N-terminal domain of the LGIC subunits and
is based on a multi-sequence ClustalX^50 alignment of 92 full-length
pentameric LGIC sequences. Alignments are shown from first to last
AChBP residue (for example, starting at second residue of mature
Torpedo alpha , beta italic gamma and delta subunits, ending approx 4
residues into the first transmembrane domain^29). H: human, T.ca:
Torpedo californica. Secondary structure elements ( alpha : alpha
-helix, beta : beta -strand, eta : 3[10]-helix) are indicated in red
above the sequence, in accordance with Fig. 3a. Precise beginnings and
ends will change with higher resolution. AChBP shares 24% sequence
identity with the ligand-binding domain (LBD) of human alpha [7] (shown
in green), 20â24% with other nicotinic receptors and 15â18% with other
LGICs. The residues conserved in the superfamily are shown in bold with
grey background. Asterisk, beginning and end of the Cys loop. Colouring
of interface residues at the plus (yellow) and minus side (light blue)
shows the lack of sequence conservation in the subunit interface across
the pentameric LGIC family. Nicotinic receptor ligand-binding residues
on the principal (pink) and complementary (dark blue) side are
indicated.
[75]High resolution image and legend (140K)
[76]Top of page
§3§ Structure determination §3§
The crystal structure of AChBP was solved using weak Pb
multiple-wavelength anomalous diffraction (MAD) data in two crystal
forms. The electron density map was improved substantially by
cross-crystal averaging of three crystal forms with 20, 10 and 5 copies
of the protomer in the asymmetric unit ([77]Table 1). The structure was
refined at 2.7 Ã
in space group P4[2]2[1]2, with one AChBP pentamer
in the asymmetric unit. Refinement with partial five-fold
non-crystallographic symmetry (NCS) restraints resulted in an R-factor
of 26.4% (R[free] = 30%).
§5§ [78] Table 1: Data collection statistics §5§
[79]Table 1 - Data collection statistics
[80]Full table
[81]Top of page
§3§ The AChBP pentamer §3§
The AChBP homopentamer, when viewed along the five-fold axis, resembles
a windmill toy, with petal-like protomers ([82]Fig. 2a). When viewed
perpendicular to the five-fold axis it forms a 62-Ã
-high cylinder
([83]Fig. 2b), with a diameter of 80 Ã
. The diameter of the central
hole is approx 18 Ã
, between side chains. These dimensions are in good
agreement with the N-terminal domain in the Torpedo nAChR electron
microscopy data^[84]21. In the pentamer the only subunit contacts are
dimer interfaces, of which each protomer has two, the plus side and the
minus side. We refer to the A (plus)âB (minus) interface as an example
for the five equivalent interfaces AB, BC, CD, DE and EA ([85]Fig. 2).
§5§ [86] Figure 2: The pentameric structure of AChBP. §5§
[87]Figure 2 : The pentameric structure of AChBP. Unfortunately we are
unable to provide accessible alternative text for this. If you require
assistance to access this image, or to obtain a text description,
please contact npg@nature.com
a, In this representation each protomer has a different colour.
Subunits are labelled anti-clockwise, with AâB, BâC, CâD, DâE and EâA
forming the plus and minus interface side, with the principal and
complementary ligand-binding sites, respectively (ball-and-stick
representation). b, Viewing the AChBP pentamer perpendicular to the
five-fold axis. The equatorially located ligand-binding site
(ball-and-stick representation) is highlighted only in the A (yellow)âB
(blue) interface.
[88]High resolution image and legend (165K)
[89]Top of page
§3§ The AChBP protomer §3§
Each AChBP protomer is a single domain protein, asymmetric in shape,
with a size of around 62 times 47 times 34 Ã
^3 ([90]Fig. 3a). It
consists of an N-terminal alpha -helix, two short 3[10] helices and a
core of ten beta -strands, which form a beta -sandwich. The order of
beta -strands conforms to a modified immunoglobulin (Ig)
topology^[91]28 ([92]Fig. 3b) with an extra beta -hairpin (f'âf") and
an extra strand (b'). These additional strands introduce two 'Greek
key' folding motifs. An Ig-like topology had been predicted for
nAChRs^[93]2, ^[94]29, but the location of the ligand-binding site was
missed, owing to the presence of extra beta -strands. Compared with the
classical Ig-fold^[95]28, the AChBP beta -strands are considerably
twisted, with the beta -sheets rotated against each other, resulting in
two separate hydrophobic cores. Thus the three-dimensional fold does
not resemble other Ig-like proteins and comparison^[96]30 with the
protein database did not result in a significant match to any known
structure.
§5§ [97] Figure 3: Overview of the AChBP protomer structure. §5§
[98]Figure 3 : Overview of the AChBP protomer structure. Unfortunately
we are unable to provide accessible alternative text for this. If you
require assistance to access this image, or to obtain a text
description, please contact npg@nature.com
a, Stereo representation of the AChBP protomer as viewed from outside
the pentameric ring. This ribbon representation is coloured as a
rainbow gradient, from blue (N terminus) to red (C terminus).
Disulphide bridges are indicated in green ball-and-stick
representation. In a complete ion channel the N terminus would point
towards the synaptic cleft and the C terminus would enter the membrane
at the bottom, continuing into the first transmembrane domain. b,
Topology diagram of the AChBP protomer. For comparison with Ig-folds
the strands have been labelled aâg, showing the additional strand (b')
and hairpin (f'âf"). In this structure, strands have been labelled beta
1â beta 10 with loops (or turns) L1âL10 preceding each strand with the
same number. The beta 5 strand is broken ( beta 5â beta 5') with
internal loop L5'; beta 6 also has a small break, but it is shown
continuously (see Fig. 1). The precise beginnings and ends of strands
may change slightly with increasing resolution, but the topology seen
here will be highly conserved across the entire family of pentameric
LGICs. S: disulphide bridge.
[99]High resolution image and legend (38K)
[100]Top of page
§3§ Positioning of functional regions §3§
In the structure, the N and C termini are located at 'top' and 'bottom'
of the pentamer, respectively. In the ion channels the transmembrane
domains are at the C-terminal end of the LBD, at the 'bottom' of the
AChBP structure ([101]Figs 2b and [102]3), starting directly at the end
of beta -strand beta 10.
In muscle type nAChRs, the main immunogenic region (MIR), comprising
residues alpha [1]67â alpha [1]76, acts as an epitope in the autoimmune
disease myasthenia gravis^[103]31. Although the MIR-related region in
AChBP (residues 65â72) has no sequence homology with the alpha
[1]-subunit, its location in a highly accessible position in loop L3 at
the 'top' of the pentamer agrees with the expected accessibility for
this region ([104]Fig. 3a). It also fits with electron microscopy
studies that located the MIR at the distal end of the receptor relative
to the membrane^[105]20.
The central pore of the pentamer is very hydrophilic, lined with
charged residues. On each AChBP promoter, a large pocket is visible,
accessible from the central pore. Each pocket, framed at the entrance
by beta -strands ( beta 3, beta 4, beta 5 and beta 5') ([106]Fig. 3a),
is uncharged and mainly hydrophobic. This region probably corresponds
to the tunnel framed by twisted beta -strands that was observed in the
alpha [1]-subunit of the Torpedo receptor at 4.6 Ã
resolution^[107]21.
There is a different cavity at each interface between the subunits.
These cavities are lined by residues, which were biochemically shown to
be involved in ligand binding in nAChRs^[108]2, ^[109]5, ^[110]6,
^[111]7, ^[112]8, ^[113]9, ^[114]10, ^[115]11, ^[116]12, ^[117]13,
^[118]14, ^[119]15, ^[120]16. These cavities are mostly buried from the
solvent, and located close to the outside of the pentameric ring
([121]Fig. 2a). When viewed perpendicular to the five-fold axis, they
are roughly equatorially positioned, about 30 Ã
away from the C termini
([122]Fig. 2b), conforming to the expected location of the Torpedo
receptor ligand-binding site, as determined by labelling^[123]32 and
electron microscopy studies^[124]18. We have concluded that these
cavities are the ligand-binding sites.
[125]Top of page
§3§ The ligand-binding site §3§
Each ligand-binding site is found in a cleft formed by a series of
loops from the principal face of one subunit and a series of beta
-strands from the complementary face of an adjacent subunit ([126]Fig.
4). The principal side on the plus side of the AB interface consists of
residues coming from loop A (Tyr A89), loop B (Trp A143, A145) and loop
C (Tyr A185, the double cysteine A187âA188 and Tyr A192) ([127]Fig.
4c). The complementary part of this binding side is formed by beta
-strands in protomer B contributing loop D (Trp B53, Gln B55), loop E
(Arg B104, Val B106, Leu B112 and Met B114) and loop F (Tyr B164)
([128]Fig. 4d). Four of the aromatic residues form the bottom half of
the cavity (Tyr A89, Tyr A185, Tyr B164 and Trp B53). The walls are
formed by Tyr A192, Trp A143, the main chain of A145, the side chains
of Met B114 and Gln B55, and the vicinal disulphide
(Cys A187âCys A188). The hydrophobic parts of Arg B104, Val B106 and
Leu B112 form the top of the binding site ([129]Fig. 4a).
§5§ [130] Figure 4: The ligand-binding site. §5§
[131]Figure 4 : The ligand-binding site. Unfortunately we are unable to
provide accessible alternative text for this. If you require assistance
to access this image, or to obtain a text description, please contact
npg@nature.com
a, Stereo representation of the ligand-binding site in ball-and-stick
representation, showing the contribution of the principal 'loops':
A (Tyr A89/ alpha [1] Tyr 93, yellow), B (Trp A143/ alpha [1] Trp 149,
dark yellow) and C (Tyr A185/ alpha [1] Tyr 190, Cys A187/ alpha [1]
Cys 192, Cys A188/ alpha [1] Cys 193, Tyr A192/ alpha [1] Tyr 198,
orange), and the complementary 'loops' D (Trp B53/ italic gamma Trp 55,
Gln B55/ italic gamma Glu 57, violet), E (Arg B104/ italic gamma
Leu 109, Val B106/ italic gamma Tyr 111, Leu B112/ italic gamma
Tyr 117, Met B114/ italic gamma Leu 119, light blue) and F (Tyr B164,
blue). b, Stereo view of the electron density map displaying a HEPES
buffer molecule in the ligand-binding site. This experimental density
(contoured at 1 sigma ) is derived from cross-crystal averaging. c,
Location of the principal ligand-binding residues (colours as in a,
orientation as in Fig. 2b). d, Location of the complementary
ligand-binding residues (colours as in a, orientation as in Fig. 2b).
Note that loops D, E and F are all on beta -strands.
[132]High resolution image and legend (89K)
All residues in the binding site have been identified by photoaffinity
labelling and mutagenesis studies^[133]6, ^[134]7, ^[135]8, ^[136]9,
^[137]10, ^[138]11, ^[139]12, ^[140]13, ^[141]14, ^[142]15, ^[143]16.
Although the side chain of His A145 is pointing away from the cavity,
its main chain is involved in the binding site. One residue identified
by labelling studies^[144]6, Trp A82 ( alpha [1] Trp 86), is involved
in hydrophobic core formation and located far from the pocket.
Therefore it probably does not participate directly in ligand binding.
Additional residues may be involved in binding large ligands such as
toxins^[145]13. Otherwise, the AChBP ligand-binding site entirely
confirms the available biochemical and mutational data on nAChRs. The
structure, however, reveals for the first time how these residues are
positioned with respect to each other, and will provide a valuable tool
for drug design studies.
All observed residues are conserved between known ligand-binding
subunits of nicotinic receptors except the loop F Tyr B164 residue. In
our structure the loop F region has an unusual conformation, but as it
is relatively weakly resolved, its precise analysis is difficult. The
loop F region has low sequence conservation in the nicotinic family
([146]Fig. 1), and in other superfamily members it may have a different
conformation, providing different residues to the binding site. Such
changes could lead to variations in affinity, for example by changing
the size of the ligand-binding site or its access route.
Close to the loop F region, the electron density was interpreted as a
calcium ion, because the crystals were grown in the presence of Ca^2+.
The cation has Asp B161, Asp B175 and the main chain of B176 as
ligands. This putative Ca^2+ ion may help to orientate Tyr B164 and
could thus be involved in ligand binding. This agrees with observations
that the residue equivalent to Asp B161 in muscle/Torpedo subunits (
italic gamma Asp 174/ delta Asp 180) is important in ligand
binding^[147]14, ^[148]15. Additionally, calcium-binding sites that
enhance the response to agonist binding have been identified in a
homologous region (residue range 161â172) of the neuronal alpha
[7]-receptor^[149]33.
The most likely access routes to the ligand-binding sites are from
above or below the double-cysteine-containing loop C ([150]Fig. 4a).
This region buries the ligand-binding site from the solvent, preventing
access from the outside. Access of some of the larger ligands, such as
d-tubocurarine, would require the binding site to be opened up, for
example by movement of the beta -hairpin beta 9â beta 10 in the C-loop
region. Access from the central pore has been suggested^[151]21, but
this would require major structural rearrangements at the interface,
which are less likely.
From the location of the ligand-binding site, we can draw conclusions
about the arrangement of ligand-binding alpha [1]-subunits with respect
to their complementary partners in the Torpedo and muscle receptors. It
has been suggested that the alpha [1] italic gamma and alpha [1] delta
interfaces occur in a clockwise alpha [1] italic gamma alpha [1] delta
beta [1] arrangement when looking towards the membrane^[152]34. Our
structure would favour an anticlockwise alpha [1] italic gamma alpha
[1]delta beta [1] arrangement, as the principal ligand-binding site is
located on the anticlockwise side of its complementary partner
([153]Fig. 2).
[154]Top of page
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To our surprise we found features of bulky electron density that
stacked onto Trp 143 in each ligand-binding site in the experimental
cross-crystal averaged electron density ([155]Fig. 4b). We have
assigned this to a HEPES
(N-2-hydroxyethylpiperazine-N'-2-ethanesulphonic acid) buffer molecule,
which contains a positively charged quaternary ammonium group and
therefore has some similarity to known nicotinic receptor ligands. Its
dissociation constant of 100 mM (data not shown) indicates that binding
under crystallization conditions (100â150 mM) is possible at low
occupancy. Although HEPES does not make any specific hydrogen bonds
with the protein, it stacks with its quaternary ammonium onto Trp 143,
making cation- pi interactions as expected for nicotinic
agonists^[156]17, ^[157]35 ([158]Fig. 4b). It buries equal amounts of
surface of the principal and complementary subunit. However, owing to
low occupancy and limited resolution of the data, the precise
orientation of the HEPES molecule cannot be definitely resolved. It has
been suggested^[159]3 that the ligand-binding site of nAChRs could be
similar to that of acetylcholinesterase (AChE). Although the size
of the binding site is roughly similar in AChBP and AChE, the observed
arrangement of aromatic residues is quite different. However, the
stacking of the quaternary ammonium of HEPES, as far as it can be
refined in the current AChBP structure, is similar to that of the
quaternary ammonium of the decamethonium in AChE on Trp 84 (ref.
[160]36).
[161]Top of page
§3§ Pentamer interface §3§
The subunit interface consists on the plus side entirely of loop
regions (L1, L2, L4, L5, L7, L8 and L10), whereas the minus side mostly
presents secondary structure elements to the interface ( alpha 1, beta
1, beta 2, beta 3, beta 5, beta 6 and L9; [162]Fig. 5). Several
residues are important for both ligand binding and pentamer formation.
The interface buries a large surface area (2,700 Ã
^2), with a mainly
uncharged character including only a single bifurcated salt bridge
(Glu A149âArg B3 and Arg B104). It is a very convoluted surface,
indicating that shape complementarity may be important in pentamer
formation ([163]Fig. 5a). The interface residues are not well conserved
between subfamilies of the superfamily of pentameric ligand-gated ion
channels ([164]Fig. 1). The residues change markedly between the
different ion-channel subtypes, with for example changes from
hydrophobic to charged and vice versa ([165]Fig. 1).
§5§ [166] Figure 5: Dimer interface. §5§
[167]Figure 5 : Dimer interface. Unfortunately we are unable to provide
accessible alternative text for this. If you require assistance to
access this image, or to obtain a text description, please contact
npg@nature.com
a, Stereo figure of the dimer interface. Representation of the
interface residues (ball-and-stick) on a schematic secondary structure.
The figure shows the plus face of subunit A (light yellow, orange
interface residues) and the minus face of subunit B (light blue, pink
interface side chains). b, Dimer interface interactions. Note that
owing to the low conservation of these interfaces (Fig. 1) the actual
interactions will not be conserved in any pentameric LGIC interface,
but that in all receptors these topological regions are likely to form
the interface.
[168]High resolution image and legend (58K)
[169]Top of page
§3§ Ligand-gated ion channels §3§
The superfamily of ligand-gated ion channels has highly conserved LBDs,
and the function and location of the conserved residues can now be
analysed in the light of the structure. Most residues that are
conserved in the superfamily ([170]Fig. 1) are hydrophobic and help to
maintain the hydrophobic core of the protomer, grouped into
three clusters ([171]Fig. 6). The first cluster is involved in packing
of the N-terminal helix alpha 1 against the main framework of the
protomer. The second cluster is situated in the upper half of the beta
-core region. The third cluster is located at the lower end of the beta
-sandwich ([172]Fig. 6). In the superfamily, two residues are conserved
in the ligand-binding site. Only very few conserved residues are
hydrophilic; two of these maintain the turns of a Greek key motif
connecting strands beta 3, beta 5, beta 6 and beta 2, in which Asp 60
stabilizes the N terminus of a small 3[10] helix and Gly 109 enables
tight-turn formation. Conserved residues Asp 85 and Asn 90 are involved
in packing of the beta -sheets. Asp 85 forms hydrogen bonds to the
highly conserved Ser 142 and Thr 144, and residue Asn 90 brings
together the main-chain oxygens of Ser 122 and Arg 137, enabling
disulphide-bond formation of the nearby absolutely conserved disulphide
bond (123â136). This disulphide bond is topologically equivalent to the
'tyrosine cornerstone'^[173]37 found in Ig-like proteins, in which
tyrosine links the two beta -sheets together, and a similar role is
fulfilled by the disulphide bond in AChBP. This structural role for the
disulphide bond explains why, in the Torpedo receptor, the
Cys 128âCys 142 bond is important for both preservation of subunit
conformational stability^[174]38 and complete nAChR assembly^[175]39.
As the conserved residues mainly contribute to the overall structure
formation, it is clear that all pentameric LGIC N-terminal domains will
have the same three-dimensional structure.
§5§ [176] Figure 6: Conservation in the pentameric LGIC superfamily. §5§
[177]Figure 6 : Conservation in the pentameric LGIC superfamily.
Unfortunately we are unable to provide accessible alternative text for
this. If you require assistance to access this image, or to obtain a
text description, please contact npg@nature.com
Conserved residues are indicated as viewed from the central pore.
Hydrophobic cluster I (red): residues 6, 10, 63, 65, 71, 81, 105, 111;
Cluster II (green): residues 20, 27, 29, 58, 82, 84, 86, 88, 140, 150,
152, 195; Cluster III (pink): residues 33, 35, 38, 41, 48, 52, 123,
125, 136, 138, 165, 171, 173, 199, 201. The hydrophilic conserved
residues (dark blue): Asp 60, Asp 85, Asn 90, Gly 109, Lys 203.
Conserved residues in the ligand-binding site (light blue): His 145,
Tyr 192, or close by: Ala 87. Very few conserved residues are at the
surface. Residues conserved between pentameric LGICs but not AChBP are
indicated by yellow main chain (14, 19, 170 and the Cys-loop124â135).
[178]High resolution image and legend (66K)
Contrary to the above residues, the Cys loop ([179]Fig. 3a) is well
conserved in the pentameric LGIC family but not in AChBP ([180]Fig. 1,
residues 129â141). It is hydrophobic in the receptors, whereas it is
hydrophilic in AChBP. The Cys loop is located at the bottom (membrane)
side of the protein, close to the dimer interface. This position, and
its hydrophobicity in the LGIC family, implies that it could interact
with the membrane or with the transmembrane region of the receptors,
functions that are absent in AChBP.
Finally, the interface region is among the least conserved regions in
the superfamily ([181]Fig. 1). Pentamer formation does not apparently
impose very stringent evolutionary requirements on these domains. The
high level of structural conservation, however, implies that the same
topological regions form these interface contacts in all superfamily
members ([182]Fig. 5b). But in these interfaces different combinations
of subunits will have different interactions, possibly creating
variations in the precise allosteric contacts and movements in the
various subclasses of these ion channels.
[183]Top of page
§3§ Activation mechanism §3§
The location of the ligand-binding site is conserved among pentameric
LGIC receptors^[184]1 but the actual ligand-binding residues vary,
creating specificity for different ligands. However, all ligand-gated
ion channel LBDs have intrinsically the same function: the activation
of a membrane pore. Indeed, a nicotinic receptor LBD is capable of
activating a serotonin membrane channel in a chimaeric
receptor^[185]40. Thus, the essential activation mechanism is conserved
across the superfamily. One option is that activation takes place by
direct rotation of the protomer through a pivoting point at the
ligand-binding site. But for any other mechanism, the location of the
conserved residues implies that transmission of a signal from the
binding pocket to the transmembrane domain takes place within the
protomer and not through the interface region.
Within the protomer, several possible regions could transmit activation
signals: changes in loop C, induced by ligand binding, could be
transmitted directly into the transmembrane domain through the beta 9â
beta 10 beta -hairpin; alternatively, large structural changes in the
beta -sheet regions could be transmitting the signal through the
conserved Cys loop, acting directly on the membrane part of the
pentameric LGICs. The movement observed at 9 Ã
for the Torpedo nAChR
upon agonist binding^[186]19 fits well with the latter suggestion. We
see a twisted beta -sandwich, with two distinct hydrophobic cores, and
it is possible that these cores move with respect to each other upon
ligand binding. The effect of any of these activation mechanisms in the
protomer will then be modulated by the varying subunit interfaces in
the different subtypes of the receptor, allowing intricate specificity
in neuronal signal transmission.
[187]Top of page
§3§ Conclusions §3§
This crystal structure shows that molluscan AChBP is a homologue of the
pentameric LGIC superfamily ligand-binding domains. It confirms the
predicted Ig-topology, the location of the binding site at the subunit
interface, the position of the MIR and the extensive data on the
nicotinic ligand-binding residues.
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