3J27

CryoEM structure of Dengue virus

PDB DOI: https://doi.org/10.2210/pdb3J27/pdb
EM Map EMD-5520: EMDB EMDataResource

Classification: VIRUS
Organism(s): dengue virus type 2
Mutation(s): No

Deposited: 2012-09-26 Released: 2012-12-19
Deposition Author(s): Zhang, X., Ge, P., Yu, X., Brannan, J.M., Bi, G., Zhang, Q., Schein, S., Zhou, Z.H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 189.81 kDa
Atom Count: 13,206
Modelled Residue Count: 1,701
Deposited Residue Count: 1,710
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, C, E	495	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944)) Explore P14340 Go to UniProtKB: P14340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14340
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small envelope protein M	B, D, F	75	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for P14340 (Dengue virus type 2 (strain Thailand/NGS-C/1944)) Explore P14340 Go to UniProtKB: P14340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14340
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 K [auth C] SDF format, chain L [auth E] SDF format, chain J [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth E] MOL2 format, chain J [auth A]	J [auth A], K [auth C], L [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 C] Focus chain L [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-19
Type: Initial release
Version 1.1: 2012-12-26
Changes: Database references
Version 1.2: 2013-01-16
Changes: Database references
Version 1.3: 2018-07-18
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3J27

CryoEM structure of Dengue virus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2