9D8X | pdb_00009d8x

Cryo-EM structure of Human Enterovirus D94 empty particle

PDB DOI: https://doi.org/10.2210/pdb9D8X/pdb
EM Map EMD-46652: EMDB EMDataResource

Classification: VIRUS
Organism(s): enterovirus D94
Mutation(s): No

Deposited: 2024-08-20 Released: 2025-09-03
Deposition Author(s): Fu, J., Klose, T., Rossmann, M.R., Kuhn, R., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9D8X

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

Literature

Structures of Human Enterovirus D94

Fu, J., Klose, T., Rossmann, M.R., vanKuppeveld, F.J.M., Kuhn, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 78.2 kDa
Atom Count: 5,329
Modeled Residue Count: 679
Deposited Residue Count: 700
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	231	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2 Go to UniProtKB: A3QWZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3QWZ2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	236	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2 Go to UniProtKB: A3QWZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3QWZ2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	233	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2 Go to UniProtKB: A3QWZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3QWZ2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI011219

Revision History (Full details and data files)

Version 1.0: 2025-09-03
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.