9MA7 | pdb_00009ma7

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9

PDB DOI: https://doi.org/10.2210/pdb9MA7/pdb
EM Map EMD-63748: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): human gammaherpesvirus 4, Homo sapiens
Expression System: Mammalian expression vector Flag-MCS-pcDNA3.1
Mutation(s): No

Deposited: 2025-03-14 Released: 2026-03-18
Deposition Author(s): Ma, H.Y., Sun, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.14 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9MA7

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

Literature

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9

Ma, H.Y., Sun, C.

To be published.

Macromolecule Content

Total Structure Weight: 204.86 kDa
Atom Count: 8,435
Modeled Residue Count: 1,111
Deposited Residue Count: 1,922
Unique protein chains: 7

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein GP350	A	478	human gammaherpesvirus 4	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03200
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1H5 heavy chain no-CH2CH3	B	248	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1H5 light chain	C	235	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
1A12 heavy chain no-CH2CH3	D	248	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
1A12 light chain	E	233	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
2E9 heavy chain no-CH2CH3	F	245	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
2E9 light chain	G	235	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.14 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U24A20743
National Natural Science Foundation of China (NSFC)	China	32441094

Revision History (Full details and data files)

Version 1.0: 2026-03-18
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.