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- PDB-8vy8: Recombinant alpha bungarotoxin complexed with HAP peptide -

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Basic information

Entry
Database: PDB / ID: 8vy8
TitleRecombinant alpha bungarotoxin complexed with HAP peptide
Components
  • Alpha-bungarotoxin isoform V31
  • HAP peptide
KeywordsTOXIN / recombinant / alpha bungarotoxin / refolded
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesBungarus multicinctus (many-banded krait)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, J. / Lei, X. / Chen, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM064642 United States
CitationJournal: Microb Cell Fact / Year: 2024
Title: Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes.
Authors: Xu, J. / Lei, X. / Li, A. / Li, J. / Li, S. / Chen, L.
History
DepositionFeb 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Alpha-bungarotoxin isoform V31
D: HAP peptide
A: Alpha-bungarotoxin isoform V31
C: HAP peptide
E: Alpha-bungarotoxin isoform V31
F: HAP peptide
G: Alpha-bungarotoxin isoform V31
H: HAP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,36111
Polymers39,6468
Non-polymers7153
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.529, 73.110, 79.840
Angle α, β, γ (deg.)90.000, 103.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...
d_3ens_1(chain "E" and ((resid 1 and (name N or name...
d_4ens_1(chain "G" and ((resid 1 and (name N or name...
d_1ens_2(chain "C" and ((resid 2 and (name N or name...
d_2ens_2(chain "D" and ((resid 2 and (name N or name...
d_3ens_2(chain "F" and ((resid 2 and (name N or name...
d_4ens_2(chain "H" and ((resid 2 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ILEILEGLNGLNAC1 - 713 - 73
d_12ens_1PROPROGLYGLYAC73 - 7475 - 76
d_21ens_1ILEILEGLNGLNBA1 - 713 - 73
d_22ens_1PROPROGLYGLYBA73 - 7475 - 76
d_31ens_1ILEILEGLNGLNEE1 - 713 - 73
d_32ens_1PROPROGLYGLYEE73 - 7475 - 76
d_41ens_1ILEILEGLNGLNGG1 - 713 - 73
d_42ens_1PROPROGLYGLYGG73 - 7475 - 76
d_11ens_2ARGARGPROPROCD2 - 122 - 12
d_21ens_2ARGARGPROPRODB2 - 122 - 12
d_31ens_2ARGARGPROPROFF2 - 122 - 12
d_41ens_2ARGARGPROPROHH2 - 122 - 12

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.99784686923, -0.012392774195, 0.0644053159033), (0.0112874443217, -0.999783188158, -0.0174977220584), (0.0646081973865, -0.0167330757574, 0.997770406961)21.5999984465, 37.3426378009, -0.468892678568
2given(-0.448712769529, -0.758652495923, 0.472338057848), (-0.136137985907, -0.464338287485, -0.875132220621), (0.883245888332, -0.456986154281, 0.105073096177)39.5648742748, 49.4588495004, -4.16989082656
3given(0.446011236483, 0.743738216922, -0.497923128224), (0.162494061575, 0.479789421093, 0.862205190984), (0.880153200803, -0.46546275479, 0.0931384293369)-17.9696996178, -12.6224876904, -3.27231526709
4given(-0.997851356093, -0.00757057003239, 0.0650796251695), (0.00620315671771, -0.999756268498, -0.0211878372005), (0.0652241672201, -0.0207386129691, 0.997655109716)21.3100698804, 37.611730072, -0.327164650293
5given(-0.422554477713, -0.745369873301, 0.515627254265), (-0.156111186338, -0.500554133416, -0.851513274717), (0.892791695114, -0.440305929435, 0.0951508152308)38.0813330816, 50.3496313102, -4.82458461029
6given(0.422758600116, 0.749799504487, -0.508994959798), (0.183991503286, 0.478942444175, 0.858347984145), (0.887368183307, -0.456524740008, 0.0645202992421)-17.9516606977, -12.6228644421, -3.19647280685

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Components

#1: Protein
Alpha-bungarotoxin isoform V31 / Alpha-BTX V31 / Alpha-Bgt(V31) / BGTX V31 / Long neurotoxin 1


Mass: 8221.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Production host: Escherichia coli (E. coli) / References: UniProt: P60616
#2: Protein/peptide
HAP peptide


Mass: 1689.843 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.01 Å3/Da / Density meas: 59.2 Mg/m3 / Density % sol: 59.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 35% PEG3350, 0.2 M MgCl2. 18 degree centigrade

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→53.2 Å / Num. obs: 18053 / % possible obs: 96.32 % / Redundancy: 7.6 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1477 / Net I/σ(I): 10.58
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.4164 / Num. unique obs: 1768 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→53.2 Å / SU ML: 0.3658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 984 5.45 %
Rwork0.2369 17060 -
obs0.239 18044 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 45 227 2943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742796
X-RAY DIFFRACTIONf_angle_d1.16643809
X-RAY DIFFRACTIONf_chiral_restr0.0518404
X-RAY DIFFRACTIONf_plane_restr0.0106478
X-RAY DIFFRACTIONf_dihedral_angle_d15.7087411
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.528250573745
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.995813594352
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.909925221876
ens_2d_2DCX-RAY DIFFRACTIONTorsion NCS0.675163474528
ens_2d_3DCX-RAY DIFFRACTIONTorsion NCS0.931897246119
ens_2d_4DCX-RAY DIFFRACTIONTorsion NCS0.923814312046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.36781250.28682394X-RAY DIFFRACTION94.77
2.53-2.680.32421420.27682390X-RAY DIFFRACTION95.15
2.68-2.890.30031470.25862402X-RAY DIFFRACTION96.04
2.89-3.180.30291500.2442433X-RAY DIFFRACTION96.67
3.18-3.640.28121220.22332457X-RAY DIFFRACTION96.48
3.64-4.590.22021420.20622465X-RAY DIFFRACTION97.86
4.59-53.20.25191560.22872519X-RAY DIFFRACTION97.49

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