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- PDB-8sm1: CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN... -

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Basic information

Entry
Database: PDB / ID: 8sm1
TitleCRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350
Components
  • 769A9 Fab heavy chain
  • 769A9 Fab light chain
  • Envelope glycoprotein gp350
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / receptor ligand activity / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Envelope glycoprotein GP350
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsChen, W.-H. / Bu, W. / Cohen, J.I. / Kanekiyo, M. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-11-2-0174 United States
CitationJournal: Immunity / Year: 2025
Title: Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.
Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, ...Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, M. / McDermott, A.B. / Nabel, G.J. / Kwong, P.D. / Mascola, J.R. / Cohen, J.I. / Kanekiyo, M.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 19, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp350
H: 769A9 Fab heavy chain
L: 769A9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,30812
Polymers94,4463
Non-polymers1,8629
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint3 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.082, 54.683, 137.220
Angle α, β, γ (deg.)90.00, 111.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody 769A9 Fab heavy chain


Mass: 24115.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 769A9 Fab light chain


Mass: 23435.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 9 molecules G

#1: Protein Envelope glycoprotein gp350 / Membrane antigen / MA


Mass: 46895.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BLLF1 / Production host: Homo sapiens (human) / References: UniProt: P03200
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.285→50 Å / Num. obs: 16984 / % possible obs: 83 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.09
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.703 / Num. unique obs: 1486

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H6O

2h6o


Resolution: 3.29→45.78 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 732 5 %
Rwork0.258 --
obs0.26 14648 82.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.59 Å2
Refinement stepCycle: LAST / Resolution: 3.29→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 118 1 6513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026696
X-RAY DIFFRACTIONf_angle_d0.6029135
X-RAY DIFFRACTIONf_dihedral_angle_d12.5413949
X-RAY DIFFRACTIONf_chiral_restr0.0441064
X-RAY DIFFRACTIONf_plane_restr0.0041161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.53820.3351820.33011576X-RAY DIFFRACTION48
3.5382-3.89410.3731330.30552508X-RAY DIFFRACTION75
3.8941-4.45720.28711630.25913102X-RAY DIFFRACTION94
4.4572-5.61390.26571740.233303X-RAY DIFFRACTION98
5.6139-45.780.29691800.24863427X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4446-0.09490.37931.30750.53754.27430.08820.260.05760.0464-0.054-0.0653-0.18130.193-0.05020.27870.0227-0.00040.28650.00110.353920.1824-84.275435.1943
21.1874-1.0096-0.54050.74510.89333.83890.26330.14580.1058-0.4763-0.1027-0.4175-1.0004-0.3875-0.11650.64410.00820.16160.52820.01240.648120.7245-93.476-15.7755
32.0721-0.4167-1.41641.24541.423.8506-0.196-0.0244-0.26140.24490.11510.02820.62350.25990.05490.4930.0552-0.01480.47410.05890.606227.3249-111.2557-18.4331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'G' AND (RESID 4 THROUGH 423 )
2X-RAY DIFFRACTION2CHAIN 'H' AND (RESID 1 THROUGH 205 )
3X-RAY DIFFRACTION3CHAIN 'L' AND (RESID 1 THROUGH 213 )

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