8DAN

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor

PDB DOI: https://doi.org/10.2210/pdb8DAN/pdb
EM Map EMD-27271: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Western equine encephalitis virus, Asarcornis scutulata
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-06-13 Released: 2023-12-20
Deposition Author(s): Zimmerman, M.I., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.74 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

Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion

Zimmerman, O., Zimmerman, M.I., Nelson, C.A., Raju, S., Errico, J.M., Madden, E.A., Hassan, A.O., VanBlargan, L.A., Kim, A.S., Adams, L.J., Basore, K., Whitener, B.M., Earnest, J.T., Holmes, A.C., Ebel, G.D., Zmasek, C., Scheuermann, R.H., Fremont, D.H., Diamond, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 498.56 kDa
Atom Count: 35,000
Modelled Residue Count: 4,472
Deposited Residue Count: 4,472
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 envelope glycoprotein	A, D, G, J	438	Western equine encephalitis virus	Mutation(s): 0 Membrane Entity: Yes
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: 1	Glycosylation Focus chain A Focus chain D Focus chain G Focus chain J
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 envelope glycoprotein	B, E, H, K	415	Western equine encephalitis virus	Mutation(s): 0 Membrane Entity: Yes
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: 1	Glycosylation Focus chain B Focus chain E Focus chain H Focus chain K
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix remodeling-associated protein 8	C, F, I, L	265	Asarcornis scutulata	Mutation(s): 0 Gene Names: Mxra8, ASASCU_R01628 Membrane Entity: Yes
UniProt
Find proteins for A0A7K7KW08 (Asarcornis scutulata) Explore A0A7K7KW08 Go to UniProtKB: A0A7K7KW08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7K7KW08
Sequence Annotations Expand
Reference Sequence

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 M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain S [auth G] SDF format, chain V [auth J] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth G] MOL2 format, chain V [auth J] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]