8SGN

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

PDB DOI: https://doi.org/10.2210/pdb8SGN/pdb

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

Deposited: 2023-04-12 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: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.193
R-Value Observed: 0.195

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 Cy651H02, 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: 97.43 kDa
Atom Count: 6,884
Modelled Residue Count: 837
Deposited Residue Count: 868
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy651H02 Fab light chain	A [auth L]	214	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cy651H02 Fab heavy chain	B [auth H]	223	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 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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth K]	2		N-Glycosylation	Interactions Focus chain D [auth K] Interactions & Density Focus chain D [auth K]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], FA [auth G], X [auth G], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain R [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain R [auth H]	G [auth L], H [auth L], I [auth L], R [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain R [auth H] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain R [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain J [auth L] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain Q [auth H] SDF format, chain S [auth H] SDF format, chain E [auth L] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain JA [auth G] SDF format, chain K [auth L] SDF format, chain KA [auth G] SDF format, chain L SDF format, chain LA [auth G] SDF format, chain M [auth L] SDF format, chain N [auth L] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain T [auth H] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain W [auth H] MOL2 format, chain F [auth L] MOL2 format, chain J [auth L] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth H] MOL2 format, chain S [auth H] MOL2 format, chain E [auth L] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth L] MOL2 format, chain KA [auth G] MOL2 format, chain L MOL2 format, chain LA [auth G] MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H]	E [auth L] F [auth L] GA [auth G] HA [auth G] IA [auth G] E [auth L], F [auth L], GA [auth G], HA [auth G], IA [auth G], J [auth L], JA [auth G], K [auth L], KA [auth G], L, LA [auth G], M [auth L], MA [auth G], N [auth L], NA [auth G], O [auth H], P [auth H], Q [auth H], S [auth H], T [auth H], U [auth H], V [auth H], W [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth L] Focus chain JA [auth G] Focus chain K [auth L] Focus chain KA [auth G] Focus chain L Focus chain LA [auth G] Focus chain M [auth L] Focus chain MA [auth G] Focus chain N [auth L] Focus chain NA [auth G] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth L] Focus chain JA [auth G] Focus chain K [auth L] Focus chain KA [auth G] Focus chain L Focus chain LA [auth G] Focus chain M [auth L] Focus chain MA [auth G] Focus chain N [auth L] Focus chain NA [auth G] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H]