8SM1

CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350

PDB DOI: https://doi.org/10.2210/pdb8SM1/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human herpesvirus 4 strain B95-8, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-04-25 Released: 2024-05-01
Deposition Author(s): Chen, W.-H., Bu, W., Cohen, J.I., Kanekiyo, M., Joyce, M.G.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.298
R-Value Work: 0.258
R-Value Observed: 0.260

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Basis For Receptor Engagement And Virus Neutralization Through Epstein-Barr Virus Gp350

Chen, W.-H., Bu, W., Cohen, J.I., Kanekiyo, M., Joyce, G.M.

To be published.

Macromolecule Content

Total Structure Weight: 96.31 kDa
Atom Count: 6,513
Modelled Residue Count: 842
Deposited Residue Count: 874
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp350	A [auth G]	431	Human herpesvirus 4 strain B95-8	Mutation(s): 0 Gene Names: BLLF1
UniProt
Find proteins for P03200 (Epstein-Barr virus (strain B95-8)) Explore P03200 Go to UniProtKB: P03200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03200
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
769A9 Fab heavy chain	B [auth H]	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
769A9 Fab light chain	C [auth L]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth G] SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain D [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] mmCIF format, chain D [auth G] mmCIF format, chain E [auth G] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain I [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G]	D [auth G] E [auth G] F [auth G] G H [auth G] D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth G] MOL2 format, chain L [auth G] mmCIF format, chain L [auth G]	L [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth G] Interactions & Density Focus chain L [auth G]