9X3K | pdb_00009x3k

apo state of Mengla Virus Glycoprotein

PDB DOI: https://doi.org/10.2210/pdb9X3K/pdb
EM Map EMD-66502: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Dianlovirus menglaense
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-10-09 Released: 2026-06-03
Deposition Author(s): Wang, L., Zou, B., Liu, B., Xue, L., He, J., Xiong, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9X3K

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

Literature

Cryo-EM Structures Reveal Mengla Virus GP uses combined Ebola- and Marburg-Like Epitope Masking Strategies to Evade Antibodies

Wang, L.Y., Zou, B.Q., Liu, B.H., Ma, Y., Xue, L., Habib, G., Yang, X.L., Chen, X.W., Zhang, Y., Yang, Z.F., He, J., Xiong, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 226.89 kDa
Atom Count: 6,885
Modeled Residue Count: 822
Deposited Residue Count: 1,986
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	A, B, C	662	Dianlovirus menglaense	Mutation(s): 0 Gene Names: GP
UniProt
Find proteins for A0A3S8UVK3 (Dianlovirus menglaense) Explore A0A3S8UVK3 Go to UniProtKB: A0A3S8UVK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3S8UVK3
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, H	6		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain H Interactions & Density Focus chain D Focus chain F Focus chain H

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Interactions & Density Focus chain E Focus chain G Focus chain I

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A], K [auth B], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16_3549
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	SRPG22-002
Other government	China	GIBHBRP24-02

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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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.