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- PDB-6n7j: BDBV223 Fab bound to synthetic peptide of Bundibugyo virus Glycop... -

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Basic information

Entry
Database: PDB / ID: 6n7j
TitleBDBV223 Fab bound to synthetic peptide of Bundibugyo virus Glycoprotein Stalk
Components
  • BDBV223 antibody heavy chain
  • BDBV223 antibody light chain
  • Envelope glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / antiviral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bundibugyo ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.684 Å
AuthorsKing, L.B. / West, B.R. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109711 United States
CitationJournal: Nat Commun / Year: 2019
Title: Cross-reactive neutralizing human survivor monoclonal antibody BDBV223 targets the ebolavirus stalk.
Authors: King, L.B. / West, B.R. / Moyer, C.L. / Gilchuk, P. / Flyak, A. / Ilinykh, P.A. / Bombardi, R. / Hui, S. / Huang, K. / Bukreyev, A. / Crowe Jr., J.E. / Saphire, E.O.
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BDBV223 antibody heavy chain
H: BDBV223 antibody heavy chain
B: BDBV223 antibody light chain
L: BDBV223 antibody light chain
C: Envelope glycoprotein
D: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)100,6296
Polymers100,6296
Non-polymers00
Water00
1
A: BDBV223 antibody heavy chain
B: BDBV223 antibody light chain
D: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,3143
Polymers50,3143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-30 kcal/mol
Surface area21180 Å2
MethodPISA
2
H: BDBV223 antibody heavy chain
L: BDBV223 antibody light chain
C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,3143
Polymers50,3143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-31 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.452, 191.580, 63.362
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody BDBV223 antibody heavy chain


Mass: 24582.586 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody BDBV223 antibody light chain


Mass: 23817.580 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein / Spike glycoprotein


Mass: 1914.183 Da / Num. of mol.: 2 / Fragment: UNP residues 620-635 / Source method: obtained synthetically / Source: (synth.) Bundibugyo ebolavirus / References: UniProt: B8XCN0
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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 20% w/v PEG8000, 0.2 M magnesium acetate, 0.1 M sodium cacodylate:HCl, pH 6.5

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Data collection

DiffractionMean temperature: 70 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.68→48.356 Å / Num. obs: 12104 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.19 / Net I/σ(I): 3.7
Reflection shellResolution: 3.68→3.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.68 / Num. unique obs: 1176 / CC1/2: 0.79 / Rpim(I) all: 0.43 / % possible all: 96.4

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MAM chains H & L

6mam


Resolution: 3.684→48.356 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.72
RfactorNum. reflection% reflection
Rfree0.254 540 4.47 %
Rwork0.2277 --
obs0.2289 12087 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.684→48.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 0 0 6913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037090
X-RAY DIFFRACTIONf_angle_d0.6799653
X-RAY DIFFRACTIONf_dihedral_angle_d15.6714229
X-RAY DIFFRACTIONf_chiral_restr0.0461078
X-RAY DIFFRACTIONf_plane_restr0.0041232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.684-4.05450.32571180.27542856X-RAY DIFFRACTION96
4.0545-4.64080.22371250.22732920X-RAY DIFFRACTION98
4.6408-5.84540.24461400.21612878X-RAY DIFFRACTION97
5.8454-48.36030.24361570.20462893X-RAY DIFFRACTION97

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