8SM0

Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350

PDB DOI: https://doi.org/10.2210/pdb8SM0/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Human herpesvirus 4 strain B95-8
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: 1.68 Å
R-Value Free: 0.241
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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: 63.8 kDa
Atom Count: 4,465
Modelled Residue Count: 529
Deposited Residue Count: 560
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement receptor type 2	A [auth C]	129	Homo sapiens	Mutation(s): 0 Gene Names: CR2, C3DR
UniProt & NIH Common Fund Data Resources
Find proteins for P20023 (Homo sapiens) Explore P20023 Go to UniProtKB: P20023
PHAROS: P20023 GTEx: ENSG00000117322
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20023
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp350	B [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

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 C SDF format, chain D [auth C] 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] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] MOL2 format, chain C MOL2 format, chain D [auth C] 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] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G]	C D [auth C] F [auth G] G H [auth G] C, D [auth C], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C Focus chain D [auth C] 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] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Interactions & Density Focus chain C Focus chain D [auth C] 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] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C]	E [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]