8SIC

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

PDB DOI: https://doi.org/10.2210/pdb8SIC/pdb

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

Deposited: 2023-04-14 Released: 2024-04-17
Deposition Author(s): Joyce, M.G., Jensen, J.L., Chen, W.H., Kanekiyo, M.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.295
R-Value Work: 0.245
R-Value Observed: 0.248

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

Joyce, M.G., Jensen, J.L., Chen, W.H., Kanekiyo, M.

To be published.

Macromolecule Content

Total Structure Weight: 190.91 kDa
Atom Count: 13,230
Modelled Residue Count: 1,696
Deposited Residue Count: 1,736
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy137C02 Fab heavy chain	A, E [auth H]	222	Macaca fascicularis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy137C02 Fab light chain	B, F [auth L]	215	Macaca fascicularis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp350	C [auth E], D [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 C [auth E] Focus chain D [auth G]
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 G [auth E] SDF format, chain H [auth E] SDF format, chain I [auth E] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth G] MOL2 format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain I [auth E] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] mmCIF format, chain G [auth E] mmCIF format, chain H [auth E] mmCIF format, chain I [auth E] mmCIF format, chain J [auth E] mmCIF format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G]	G [auth E] H [auth E] I [auth E] J [auth E] K [auth E] G [auth E], H [auth E], I [auth E], J [auth E], K [auth E], L [auth E], N [auth E], O [auth E], P [auth G], Q [auth G], R [auth G], S [auth G], T [auth G], U [auth G], V [auth G], W [auth G], X [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Interactions & Density Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain Y [auth G] MOL2 format, chain M [auth E] MOL2 format, chain Y [auth G] mmCIF format, chain M [auth E] mmCIF format, chain Y [auth G]	M [auth E], Y [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain Y [auth G] Interactions & Density Focus chain M [auth E] Focus chain Y [auth G]