9DQV | pdb_00009dqv

Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1

PDB DOI: https://doi.org/10.2210/pdb9DQV/pdb
EM Map EMD-47116: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Western equine encephalitis virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-24 Released: 2025-03-26
Deposition Author(s): Abraham, J., Fan, X., Li, W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1

Abraham, J., Fan, X., Li, W.

To be published.

Macromolecule Content

Total Structure Weight: 489.05 kDa
Atom Count: 33,701
Modelled Residue Count: 4,330
Deposited Residue Count: 4,412
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	A [auth D], D [auth G], G [auth J], M [auth A]	434	Western equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for C7EPF2 (Western equine encephalitis virus) Explore C7EPF2 Go to UniProtKB: C7EPF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7EPF2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth D] Focus chain D [auth G] Focus chain G [auth J] Focus chain M [auth A]
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	B [auth E], E [auth H], H [auth K], N [auth B]	403	Western equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for Q1W679 (Western equine encephalitis virus) Explore Q1W679 Go to UniProtKB: Q1W679
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1W679
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth E] Focus chain E [auth H] Focus chain H [auth K] Focus chain N [auth B]
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C [auth F], F [auth I], I [auth L], O [auth C]	163	Western equine encephalitis virus	Mutation(s): 0 EC: 3.4.21.90
UniProt
Find proteins for P13897 (Western equine encephalitis virus) Explore P13897 Go to UniProtKB: P13897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13897
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocadherin-10	J [auth M], K [auth N], L [auth O], P	103	Homo sapiens	Mutation(s): 0 Gene Names: PCDH10, KIAA1400
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2E7 (Homo sapiens) Explore Q9P2E7 Go to UniProtKB: Q9P2E7
PHAROS: Q9P2E7 GTEx: ENSG00000138650
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9P2E7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain CA [auth A] SDF format, chain EA [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain Z [auth J] SDF format, chain AA [auth K] SDF format, chain DA [auth A] SDF format, chain FA [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain Z [auth J] MOL2 format, chain AA [auth K] MOL2 format, chain DA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth J] mmCIF format, chain BA [auth K] mmCIF format, chain CA [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain Z [auth J] mmCIF format, chain AA [auth K] mmCIF format, chain DA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth J]	AA [auth K] BA [auth K] CA [auth A] DA [auth A] EA [auth B] AA [auth K], BA [auth K], CA [auth A], DA [auth A], EA [auth B], FA [auth B], Q [auth D], R [auth D], S [auth E], T [auth E], U [auth G], V [auth G], W [auth H], X [auth H], Y [auth J], Z [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth K] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth K] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth J] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Abraham, J.

Fan, X.

Li, W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 9DQV | pdb_00009dqv

Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1

Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9DQV | pdb_00009dqv