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- PDB-1hc9: alpha-bungarotoxin complexed with high affinity peptide -

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Open data


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Basic information

Entry
Database: PDB / ID: 1hc9
Titlealpha-bungarotoxin complexed with high affinity peptide
Components
  • ALPHA-BUNGAROTOXIN ISOFORM A31
  • ALPHA-BUNGAROTOXIN ISOFORM V31
  • PEPTIDE INHIBITOR
KeywordsTOXIN/PEPTIDE / COMPLEX (TOXIN-PEPTIDE) / ACETYLCHOLINE RECEPTOR MIMITOPE / ALPHA-BUNGAROTOXIN / 3- FINGER / PROTEIN-PEPTIDE COMPLEX / TOXIN / TOXIN-PEPTIDE complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Alpha-bungarotoxin / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesBUNGARUS MULTICINCTUS (many-banded krait)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarel, M. / Kasher, R. / Sussman, J.L.
CitationJournal: Neuron / Year: 2001
Title: The Binding Site of Acetylcholine Receptor as Visualized in the X-Ray Structure of a Complex between Alpha-Bungarotoxin and a Mimotope Peptide.
Authors: Harel, M. / Kasher, R. / Nicolas, A. / Guss, J.M. / Balass, M. / Fridkin, M. / Smit, A.B. / Brejc, K. / Sixma, T.K. / Katchalski-Katzir, E. / Sussman, J.L. / Fuchs, S.
History
DepositionMay 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2001Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Mar 22, 2017Group: Source and taxonomy
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN ISOFORM V31
B: ALPHA-BUNGAROTOXIN ISOFORM A31
C: PEPTIDE INHIBITOR
D: PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6726
Polymers19,4184
Non-polymers2542
Water3,909217
1
A: ALPHA-BUNGAROTOXIN ISOFORM V31
C: PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8503
Polymers9,7232
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9.9 kcal/mol
Surface area6220 Å2
MethodPISA
2
B: ALPHA-BUNGAROTOXIN ISOFORM A31
D: PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8223
Polymers9,6952
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9.4 kcal/mol
Surface area5930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.042, 153.356, 73.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsCOMPLEX OF THE ALPHA-BUNGAROTOXIN AND THE PEPTIDE INHIBITOR

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Components

#1: Protein ALPHA-BUNGAROTOXIN ISOFORM V31 / ALPHA-BTX V31 / ALPHA-BGT(V31) / BGTX V31 / LONG NEUROTOXIN 1


Mass: 8033.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALPHA-NEUROTOXIN / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / Secretion: VENOM / References: UniProt: P60616
#2: Protein ALPHA-BUNGAROTOXIN ISOFORM A31 / ALPHA-BTX A31 / ALPHA-BGT(A31) / BGTX A31 / LONG NEUROTOXIN 1


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / Secretion: VENOM / References: UniProt: P60615
#3: Protein/peptide PEPTIDE INHIBITOR / HIGH AFFINITY PEPTIDE


Mass: 1689.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND MIMICKS BINDING OF THE TOXIN TO THE NICOTINIC ...THE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND MIMICKS BINDING OF THE TOXIN TO THE NICOTINIC ACETYLCHOLINE RECEPTOR. RESIDUES A31 IS SEEN AS VAL WITH OCCUPANCY 0.3 AND ALA WITH OCCUPANCY 0.7, ACCORDING TO A WELL KNOWN MUTATION OF ALPHA-BUNGAROTOXIN

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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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5 / Details: 40% PEG 3350, 0.1M PIPES BUFFER PH 7.5
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
240 %PEG33501reservoir
30.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Date: Jul 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→23.5 Å / Num. obs: 19144 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.081 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.594 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 22265 / % possible obs: 99 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.594

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NTN 1-66 RESIDUES

1ntn


Resolution: 1.8→23.47 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES WITH ALTERNATE CONFORMATIONS: A12, A48, A50, A52, A56, A59, B34, B56, B71 THE 2 IODIDE IONS I1 A AND I1 B HAVE OCCUPANCY OF 0.4
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2203 9.9 %RANDOM
Rwork0.202 ---
obs0.202 22236 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.3 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2--2.34 Å20 Å2
3----4.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 2 217 1556
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 376 10.4 %
Rwork0.293 3256 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 22265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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