5F4M

Protruding domain of GII.17 norovirus Kawasaki323

PDB DOI: https://doi.org/10.2210/pdb5F4M/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus 13-BH-1/2013/GII.17
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-12-03 Released: 2016-01-13
Deposition Author(s): Singh, B.K., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.187
R-Value Work: 0.159
R-Value Observed: 0.161

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural Evolution of the Emerging 2014-2015 GII.17 Noroviruses.

Singh, B.K., Koromyslova, A., Hefele, L., Gurth, C., Hansman, G.S.

(2015) J Virol 90: 2710-2715

PubMed: 26699640 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.03119-15
Primary Citation of Related Structures:
5F4J, 5F4M, 5F4O

PubMed Abstract:
Recent reports suggest that human genogroup II genotype 17 (GII.17) noroviruses are increasing in prevalence. We analyzed the evolutionary changes of three GII.17 capsid protruding (P) domains. We found that the GII.17 P domains had little cross-reactivity with antisera raised against the dominant GII.4 strains. X-ray structural analysis of GII.17 P domains from 2002 to 2014 and 2015 suggested that surface-exposed substitutions on the uppermost part of the P domain might have generated a novel 2014-2015 GII.17 variant.

Organizational Affiliation

Schaller Research Group, University of Heidelberg and DKFZ, Heidelberg, Germany Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 68.3 kDa
Atom Count: 5,145
Modelled Residue Count: 613
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	308	Norovirus 13-BH-1/2013/GII.17	Mutation(s): 0
UniProt
Find proteins for A0A0A7CJV4 (Norovirus 13-BH-1/2013/GII.17) Explore A0A0A7CJV4 Go to UniProtKB: A0A0A7CJV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A7CJV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.187
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.51	α = 90
b = 121.51	β = 90
c = 156.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Singh, B.K.

Hansman, G.S.

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-02-24
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description