PDB-1yi5: Crystal structure of the a-cobratoxin-AChBP complex

ID or keywords:

Entry

Database: PDB / ID: 1yi5

Title

Crystal structure of the a-cobratoxin-AChBP complex

Components

Acetylcholine-binding protein
Long neurotoxin 1

Keywords

TOXIN / acetylcholine binding protein / snake three-fingered alpha-neurotoxin

Function / homology

Function and homology information

acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / toxin activity / postsynapse / neuron projection / extracellular region / membrane
Similarity search - Function

Biological species

Lymnaea stagnalis (great pond snail)

Naja siamensis (cobra)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.2 Å

Authors

Bourne, Y. / Talley, T.T. / Hansen, S.B. / Taylor, P. / Marchot, P.

Citation

Journal: Embo J. / Year: 2005
Title: Crystal structure of a Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors
Authors: Bourne, Y. / Talley, T.T. / Hansen, S.B. / Taylor, P. / Marchot, P.

History

Deposition	Jan 11, 2005	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 17, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 25, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1yi5.cif.gz	256.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1yi5.ent.gz	208 KB	Display	PDB format
PDBx/mmJSON format	1yi5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yi/1yi5 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/1yi5	HTTPS FTP

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Related structure data

Related structure data	1ux2S 2ctxS 1i9b 1uv6 1uw6 S: Starting model for refinement
Similar structure data	4hqp-d 3vvb-1 1st6-d 4f0q-d 4kh4-d 4f0p-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#71 - Nov 2005 Acetylcholine Receptor similarity (10) #54 - Jun 2004 Acetylcholinesterase similarity (3) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4)

Deposited unit

A: Acetylcholine-binding protein

F: Long neurotoxin 1

B: Acetylcholine-binding protein

G: Long neurotoxin 1

C: Acetylcholine-binding protein

H: Long neurotoxin 1

D: Acetylcholine-binding protein

I: Long neurotoxin 1

E: Acetylcholine-binding protein

J: Long neurotoxin 1

159 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	162.604, 313.415, 106.548
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	A
7	1	B
8	1	C
9	1	D
10	1	E
1	2	F
2	2	G
3	2	H
4	2	I
5	2	J

NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	PRO	PRO	A	A	1 - 154	1 - 154
2	1	1	LEU	LEU	PRO	PRO	B	C	1 - 154	1 - 154
3	1	1	LEU	LEU	PRO	PRO	C	E	1 - 154	1 - 154
4	1	1	LEU	LEU	PRO	PRO	D	G	1 - 154	1 - 154
5	1	1	LEU	LEU	PRO	PRO	E	I	1 - 154	1 - 154
6	2	1	GLU	GLU	ARG	ARG	A	A	163 - 202	163 - 202
7	2	1	GLU	GLU	ARG	ARG	B	C	163 - 202	163 - 202
8	2	1	GLU	GLU	ARG	ARG	C	E	163 - 202	163 - 202
9	2	1	GLU	GLU	ARG	ARG	D	G	163 - 202	163 - 202
10	2	1	GLU	GLU	ARG	ARG	E	I	163 - 202	163 - 202
1	1	2	ILE	ILE	PRO	PRO	F	B	1 - 66	1 - 66
2	1	2	ILE	ILE	PRO	PRO	G	D	1 - 66	1 - 66
3	1	2	ILE	ILE	PRO	PRO	H	F	1 - 66	1 - 66
4	1	2	ILE	ILE	PRO	PRO	I	H	1 - 66	1 - 66
5	1	2	ILE	ILE	PRO	PRO	J	J	1 - 66	1 - 66

NCS ensembles :

ID
1
2

#1: Protein	Acetylcholine-binding protein / ACh-binding protein / AchBP Mass: 23862.523 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Lymnaea stagnalis (great pond snail) / Strain: HEK 293 cells / References: UniProt: P58154
#2: Protein	Long neurotoxin 1 / Neurotoxin 3 / Alpha-cobratoxin Mass: 7842.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Naja siamensis (cobra) / Secretion: venom / References: UniProt: P01391

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.1 Å³/Da / Density % sol: 70 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.9M NA-CITRATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.975 Å / Relative weight: 1
Reflection	Resolution: 4.2→30 Å / Num. all: 57939 / Num. obs: 19232 / % possible obs: 95.1 % / Redundancy: 3.1 % / B_iso Wilson estimate: 41.1 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 4.5

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
CCP4	(SCALA)	data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UX2, 2CTX

1ux2

2ctx

Resolution: 4.2→30 Å / Cor.coef. F_o:F_c: 0.787 / Cor.coef. F_o:F_c free: 0.734 / SU B: 89.608 / SU ML: 1.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.37796	981	5.1 %	RANDOM
R_work	0.33101	-	-	-
obs	0.33339	18240	94.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 37.989 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	18.4 Å²	0 Å²	0 Å²
2-	-	-10.39 Å²	0 Å²
3-	-	-	-8.01 Å²

Refinement step

Cycle: LAST / Resolution: 4.2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10648	0	0	0	10648

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	10915
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9541
X-RAY DIFFRACTION	r_angle_refined_deg	1.405	1.937	14906
X-RAY DIFFRACTION	r_angle_other_deg	0.885	3	22282
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.465	5	1342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1708
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	12050
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2161
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	2283
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	11353
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	7223
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	186
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.12	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.216	0.2	66
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.082	1.5	6801
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.173	2	11179
X-RAY DIFFRACTION	r_scbond_it	0.301	3	4114
X-RAY DIFFRACTION	r_scangle_it	0.497	4.5	3727
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1148	tight positional	0.03	0.05
1	2	B	1148	tight positional	0.03	0.05
1	3	C	1148	tight positional	0.03	0.05
1	4	D	1148	tight positional	0.03	0.05
1	5	E	1148	tight positional	0.03	0.05
2	1	F	386	tight positional	0.03	0.05
2	2	G	386	tight positional	0.03	0.05
2	3	H	386	tight positional	0.03	0.05
2	4	I	386	tight positional	0.03	0.05
2	5	J	386	tight positional	0.03	0.05
1	1	A	1817	medium positional	0.38	0.5
1	2	B	1817	medium positional	0.39	0.5
1	3	C	1817	medium positional	0.41	0.5
1	4	D	1817	medium positional	0.38	0.5
1	5	E	1817	medium positional	0.4	0.5
2	1	F	544	medium positional	0.5	0.5
2	2	G	544	medium positional	0.31	0.5
2	3	H	544	medium positional	0.32	0.5
2	4	I	544	medium positional	0.38	0.5
2	5	J	544	medium positional	0.35	0.5
1	1	A	1148	tight thermal	0.02	0.5
1	2	B	1148	tight thermal	0.02	0.5
1	3	C	1148	tight thermal	0.02	0.5
1	4	D	1148	tight thermal	0.02	0.5
1	5	E	1148	tight thermal	0.02	0.5
2	1	F	386	tight thermal	0.03	0.5
2	2	G	386	tight thermal	0.03	0.5
2	3	H	386	tight thermal	0.03	0.5
2	4	I	386	tight thermal	0.03	0.5
2	5	J	386	tight thermal	0.03	0.5
1	1	A	1817	medium thermal	0.13	2
1	2	B	1817	medium thermal	0.14	2
1	3	C	1817	medium thermal	0.14	2
1	4	D	1817	medium thermal	0.14	2
1	5	E	1817	medium thermal	0.15	2
2	1	F	544	medium thermal	0.13	2
2	2	G	544	medium thermal	0.15	2
2	3	H	544	medium thermal	0.2	2
2	4	I	544	medium thermal	0.17	2
2	5	J	544	medium thermal	0.21	2

LS refinement shell

Resolution: 4.2→4.307 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.443	57
R_work	0.367	1205

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.6713	2.3854	-0.9499	2.8351	-0.4062	2.5196	-0.1	-0.0424	0.4453	0.5369	-0.0355	-0.0865	0.098	0.1836	0.1356	0.0955	0	0	0.0955	0	0.0955	113.3903	215.6967	86.7361
2	4.2217	0.9474	0.8227	1.369	-0.3132	1.9158	0.0121	-0.3817	0.3652	0.5402	-0.193	-0.2704	0.2281	0.2194	0.181	0.0955	0	0	0.0955	0	0.0955	113.9472	193.9218	102.7733
3	1.4027	-0.2796	1.3065	1.7546	0.1008	2.2997	0.0676	-0.4013	-0.2451	-0.0293	0.0349	-0.2096	0.3646	0.2671	-0.1025	0.0883	-0.0422	-0.0794	0.0948	-0.0006	0.0913	114.0432	172.1732	86.8524
4	2.6627	-0.8651	-0.666	2.1263	-0.1716	1.9303	0.0973	0.3546	-0.3835	-0.6878	-0.0293	-0.1396	0.1134	0.2803	-0.0679	0.0955	0	0	0.0955	0	0.0954	113.5764	180.1148	61.0417
5	3.0481	0.8816	-1.1772	2.8824	-0.1291	2.1242	0.0329	0.7034	0.401	-0.0454	0.0447	-0.179	-0.171	0.2588	-0.0776	0.0955	0	0	0.0954	0.0001	0.0955	113.1287	207.2823	61.0173
6	0.8624	0.028	-0.0937	0.1218	-0.0991	-0.5036	0.0722	0.1563	0.1233	0.0866	-0.0548	0.0801	-0.0433	-0.0422	-0.0175	0.0921	-0.0225	0.0823	0.1464	0.0342	0.1047	112.2945	193.8499	79.9338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 205	1 - 205
2	X-RAY DIFFRACTION	2	B	C	1 - 205	1 - 205
3	X-RAY DIFFRACTION	3	C	E	1 - 206	1 - 206
4	X-RAY DIFFRACTION	4	D	G	1 - 205	1 - 205
5	X-RAY DIFFRACTION	5	E	I	1 - 205	1 - 205
6	X-RAY DIFFRACTION	6	F	B	1 - 68	1 - 68
7	X-RAY DIFFRACTION	6	G	D	1 - 68	1 - 68
8	X-RAY DIFFRACTION	6	H	F	1 - 68	1 - 68
9	X-RAY DIFFRACTION	6	I	H	1 - 67	1 - 67
10	X-RAY DIFFRACTION	6	J	J	1 - 68	1 - 68

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