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- PDB-8awm: RVFV GnH with Fab268 bound -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8awm
TitleRVFV GnH with Fab268 bound
Components
  • Glycoprotein
  • Heavy chain Fab268
  • Light chain Fab268
KeywordsVIRAL PROTEIN / RVFV / Gn / Fab268
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Immunoglobulins ...Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Rift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHulswit, R.J.G. / Bowden, T.A. / Stass, R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V031635/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Multifunctional human monoclonal antibody combination mediates protection against Rift Valley fever virus at low doses.
Authors: Chapman, N.S. / Hulswit, R.J.G. / Westover, J.L.B. / Stass, R. / Paesen, G.C. / Binshtein, E. / Reidy, J.X. / Engdahl, T.B. / Handal, L.S. / Flores, A. / Gowen, B.B. / Bowden, T.A. / Crowe Jr., J.E.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain Fab268
L: Light chain Fab268
A: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)82,4773
Polymers82,4773
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-26 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.072, 98.587, 123.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy chain Fab268


Mass: 23633.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Light chain Fab268


Mass: 22768.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Glycoprotein


Mass: 36075.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A2T080
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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bis-tris pH 5.5, 25% w/v PEG 3,350 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→61.57 Å / Num. obs: 10540 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.992 / Rmerge(I) obs: 0.56 / Net I/σ(I): 2.7
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 2.004 / Num. unique obs: 558 / CC1/2: 0.789 / Rpim(I) all: 0.569

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f8p

6f8p


Resolution: 3.5→61.57 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 540 5.14 %
Rwork0.2466 9972 -
obs0.2482 10512 89.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.68 Å2 / Biso mean: 80.8076 Å2 / Biso min: 42.64 Å2
Refinement stepCycle: final / Resolution: 3.5→61.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 0 0 5538
Num. residues----726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.850.34881440.32462362250687
3.85-4.410.32981270.25812426255389
4.41-5.550.24941360.23012534267091
5.56-61.570.22981330.21592650278391

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