9MVE | pdb_00009mve

Dengue virus serotype-3 (DENV3) complex with DC-SIGN CRD at 4C

PDB DOI: https://doi.org/10.2210/pdb9MVE/pdb
EM Map EMD-48666: EMDB EMDataResource

Classification: VIRUS
Organism(s): dengue virus type 3, Homo sapiens
Expression System: Aedes albopictus, Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-01-15 Released: 2026-07-22
Deposition Author(s): Are, V.N., Fokine, A., Klose, T., Kuhn, R.J., 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: 3.40 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

Cryo-EM structures and biochemical assays demonstrate dengue viruses utilize heparin and glycan binding receptor DC-SIGN for infection

Are, V.N., Kuhn, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 252.82 kDa
Atom Count: 16,317
Modeled Residue Count: 2,097
Deposited Residue Count: 2,280
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, C, E	493	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q6DRA0 (Dengue virus type 3) Explore Q6DRA0 Go to UniProtKB: Q6DRA0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DRA0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M protein	B, D, F	75	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q6DRA0 (Dengue virus type 3) Explore Q6DRA0 Go to UniProtKB: Q6DRA0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DRA0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DC-SIGN CRD	G [auth K], H [auth J], I [auth L]	192	Homo sapiens	Mutation(s): 0 Gene Names: CD209, CLEC4L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NNX6 (Homo sapiens) Explore Q9NNX6 Go to UniProtKB: Q9NNX6
GTEx: ENSG00000090659
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NNX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain N [auth E] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain O [auth E] MOL2 format, chain N [auth E] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain O [auth E] mmCIF format, chain N [auth E] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth C] M [auth C] N [auth E] J [auth A], K [auth A], L [auth C], M [auth C], N [auth E], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth E]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth L] SDF format, chain V [auth L] SDF format, chain U [auth J] SDF format, chain T [auth J] SDF format, chain S [auth J] SDF format, chain R [auth K] SDF format, chain Q [auth K] SDF format, chain P [auth K] MOL2 format, chain X [auth L] MOL2 format, chain W [auth L] MOL2 format, chain V [auth L] MOL2 format, chain U [auth J] MOL2 format, chain T [auth J] MOL2 format, chain S [auth J] MOL2 format, chain R [auth K] MOL2 format, chain Q [auth K] MOL2 format, chain P [auth K] mmCIF format, chain X [auth L] mmCIF format, chain W [auth L] mmCIF format, chain V [auth L] mmCIF format, chain U [auth J] mmCIF format, chain T [auth J] mmCIF format, chain S [auth J] mmCIF format, chain R [auth K] mmCIF format, chain Q [auth K] mmCIF format, chain P [auth K]	P [auth K] Q [auth K] R [auth K] S [auth J] T [auth J] P [auth K], Q [auth K], R [auth K], S [auth J], T [auth J], U [auth J], V [auth L], W [auth L], X [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth K] Focus chain Q [auth K] Focus chain R [auth K] Focus chain S [auth J] Focus chain T [auth J] Focus chain U [auth J] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Interactions & Density Focus chain P [auth K] Focus chain Q [auth K] Focus chain R [auth K] Focus chain S [auth J] Focus chain T [auth J] Focus chain U [auth J] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L]