9DQZ | pdb_00009dqz

Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR

PDB DOI: https://doi.org/10.2210/pdb9DQZ/pdb
EM Map EMD-47119: 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: 2.90 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 McMillan VLP in complex with human VLDLR

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

To be published.

Macromolecule Content

Total Structure Weight: 478.71 kDa
Atom Count: 33,465
Modeled Residue Count: 4,327
Deposited Residue Count: 4,332
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]	438	Western equine encephalitis virus	Mutation(s): 0
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
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

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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]	409	Western equine encephalitis virus	Mutation(s): 0
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
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

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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]	158	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Very low-density lipoprotein receptor	J [auth M], K [auth N], L [auth O], P	78	Homo sapiens	Mutation(s): 0 Gene Names: VLDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens) Explore P98155 Go to UniProtKB: P98155
PHAROS: P98155 GTEx: ENSG00000147852
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P98155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 IA [auth A] SDF format, chain JA [auth A] SDF format, chain LA [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth G] SDF format, chain Y [auth J] SDF format, chain Z [auth J] SDF format, chain X [auth H] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain KA [auth B] SDF format, chain AA [auth K] MOL2 format, chain BA [auth K] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth G] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] MOL2 format, chain X [auth H] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain KA [auth B] MOL2 format, chain AA [auth K] mmCIF format, chain BA [auth K] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain V [auth G] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J] mmCIF format, chain X [auth H] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain KA [auth B] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth K] IA [auth A] JA [auth A] KA [auth B] AA [auth K], BA [auth K], IA [auth A], JA [auth A], KA [auth B], LA [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 IA [auth A] Focus chain JA [auth A] Focus chain KA [auth B] Focus chain LA [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 IA [auth A] Focus chain JA [auth A] Focus chain KA [auth B] Focus chain LA [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]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth M] SDF format, chain DA [auth M] SDF format, chain EA [auth N] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain HA [auth O] SDF format, chain NA [auth P] SDF format, chain MA [auth P] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth O] MOL2 format, chain NA [auth P] MOL2 format, chain MA [auth P] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain EA [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth O] mmCIF format, chain NA [auth P] mmCIF format, chain MA [auth P]	CA [auth M] DA [auth M] EA [auth N] FA [auth N] GA [auth O] CA [auth M], DA [auth M], EA [auth N], FA [auth N], GA [auth O], HA [auth O], MA [auth P], NA [auth P]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth O] Focus chain MA [auth P] Focus chain NA [auth P] Interactions & Density Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth O] Focus chain MA [auth P] Focus chain NA [auth P]

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	1.21rc1_5127:

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	--