8X0K | pdb_00008x0k

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

PDB DOI: https://doi.org/10.2210/pdb8X0K/pdb
EM Map EMD-37980: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Semliki Forest virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-11-04 Released: 2024-11-27
Deposition Author(s): Gao, F.G., Liu, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

Gao, F.G., Liu, S.

To be published.

Macromolecule Content

Total Structure Weight: 467.94 kDa
Atom Count: 32,740
Modeled Residue Count: 4,220
Deposited Residue Count: 4,220
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, D [auth E], G [auth I], J [auth M]	162	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E2	B, E [auth F], H [auth J], K [auth N]	418	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain E [auth F] Focus chain H [auth J] Focus chain K [auth N]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	C, F [auth G], I [auth K], L [auth O]	438	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain F [auth G] Focus chain I [auth K] Focus chain L [auth O]
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	M [auth D], N [auth H], O [auth L], P	37	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

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q, R, S, T, U Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 Z [auth G] SDF format, chain Y [auth C] SDF format, chain BA [auth O] SDF format, chain AA [auth K] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain BA [auth O] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain BA [auth O] mmCIF format, chain AA [auth K]	AA [auth K], BA [auth O], Y [auth C], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth O] Focus chain Y [auth C] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth O] Focus chain Y [auth C] Focus chain Z [auth G]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth P] SDF format, chain EA [auth L] SDF format, chain DA [auth H] SDF format, chain CA [auth D] MOL2 format, chain FA [auth P] MOL2 format, chain EA [auth L] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth D] mmCIF format, chain FA [auth P] mmCIF format, chain EA [auth L] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth D]	CA [auth D], DA [auth H], EA [auth L], FA [auth P]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth H] Focus chain EA [auth L] Focus chain FA [auth P] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth H] Focus chain EA [auth L] Focus chain FA [auth P]