5LFE | pdb_00005lfe

Protruding domain of GII.4 human norovirus isolate 8-14 in complex with HBGA type B (triglycan)

PDB DOI: https://doi.org/10.2210/pdb5LFE/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-01 Released: 2017-07-12
Deposition Author(s): Singh, B.K., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.233 (Depositor), 0.235 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LFE

This is version 2.1 of the entry. See complete history.

Literature

Four decades of structural evolution of GII.4 norovirus

Singh, B.K., Hansman, G.S.

To be published.

Macromolecule Content

Total Structure Weight: 68.88 kDa
Atom Count: 5,131
Modeled Residue Count: 615
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	309	Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU	Mutation(s): 0
UniProt
Find proteins for M4QNL3 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU) Explore M4QNL3 Go to UniProtKB: M4QNL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M4QNL3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G11065GA GlyCosmos: G11065GA GlyGen: G11065GA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.277 (Depositor), 0.277 (DCC)
R-Value Work: 0.233 (Depositor), 0.235 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.83	α = 90
b = 55.42	β = 99.38
c = 87.1	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: 2017-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.