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- PDB-4hqp: Alpha7 nicotinic receptor chimera and its complex with Alpha bung... -

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Basic information

Entry
Database: PDB / ID: 4hqp
TitleAlpha7 nicotinic receptor chimera and its complex with Alpha bungarotoxin
Components
  • Alpha-bungarotoxin isoform V31
  • Alpha7 nicotinic receptor chimera
KeywordsPROTEIN BINDING / Protein-protein Complex / nicotinic receptor / Membrane / nAChR / a-bungarotoxin
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmembrane signaling receptor activity / toxin activity / synapse / extracellular region / membrane
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel ...Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Ribbon / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Acetylcholine-binding protein / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesHomo sapiens (human)
Lymnaea stagnalis (great pond snail)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsLi, S.X. / Cheng, K. / Gomoto, R. / Bren, N. / Huang, S. / Sine, S. / Chen, L.
CitationJournal: To be Published
Title: Structural principles for Alpha-neurotoxin binding to and selectivity among nicotinic receptors
Authors: Li, S.X. / Cheng, K. / Gomoto, R. / Bren, N. / Huang, S. / Sine, S. / Chen, L.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha7 nicotinic receptor chimera
B: Alpha7 nicotinic receptor chimera
C: Alpha7 nicotinic receptor chimera
D: Alpha7 nicotinic receptor chimera
E: Alpha7 nicotinic receptor chimera
F: Alpha-bungarotoxin isoform V31
G: Alpha-bungarotoxin isoform V31
H: Alpha-bungarotoxin isoform V31
I: Alpha-bungarotoxin isoform V31
J: Alpha-bungarotoxin isoform V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,45617
Polymers156,70410
Non-polymers1,7527
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23960 Å2
ΔGint-64 kcal/mol
Surface area59020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.150, 142.150, 518.135
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Alpha7 nicotinic receptor chimera


Mass: 23364.502 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Lymnaea stagnalis / Production host: Pichia pastoris (fungus) / References: UniProt: P58154*PLUS
#2: Protein
Alpha-bungarotoxin isoform V31 / Alpha-BTX V31 / Alpha-Bgt(V31) / BGTX V31 / Long neurotoxin 1


Mass: 7976.282 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / Organ: venom / References: UniProt: P60616
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsCHIMERIC PROTEIN BASED ON UNP ENTRIES P58154, P36544

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.49 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONAPS 23-ID-B21
SYNCHROTRONAPS 21-ID-D31
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
MARMOSAIC 300 mm CCD2CCD
MARMOSAIC 300 mm CCD3CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
3x-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→45.8 Å / Num. obs: 38979

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Processing

SoftwareName: CNS / Version: 1.3 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.51→45.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 8459685.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.321 3912 10 %RANDOM
Rwork0.311 ---
obs0.311 38979 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 106.173 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 159.7 Å2
Baniso -1Baniso -2Baniso -3
1-22.74 Å20 Å20 Å2
2--22.74 Å20 Å2
3----45.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.67 Å
Luzzati d res low-5 Å
Luzzati sigma a1.18 Å1.12 Å
Refinement stepCycle: LAST / Resolution: 3.51→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10980 0 112 0 11092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.411.5
X-RAY DIFFRACTIONc_mcangle_it0.752
X-RAY DIFFRACTIONc_scbond_it0.22
X-RAY DIFFRACTIONc_scangle_it0.412.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 592 10.3 %
Rwork0.433 5142 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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