5HZA | pdb_00005hza

Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 FL)

PDB DOI: https://doi.org/10.2210/pdb5HZA/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus GII.10
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-02-02 Released: 2016-03-02
Deposition Author(s): Hansman, G.S., Koromyslova, A.D., Singh, B.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.179 (Depositor), 0.179 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides.

Weichert, S., Koromyslova, A., Singh, B.K., Hansman, S., Jennewein, S., Schroten, H., Hansman, G.S.

(2016) J Virol 90: 4843-4848

PubMed: 26889023 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.03223-15
Primary Citation Related Structures:
5HZA, 5HZB

PubMed Abstract:
Histo-blood group antigens (HBGAs) are important binding factors for norovirus infections. We show that two human milk oligosaccharides, 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL), could block norovirus from binding to surrogate HBGA samples. We found that 2'FL and 3FL bound at the equivalent HBGA pockets on the norovirus capsid using X-ray crystallography. Our data revealed that 2'FL and 3FL structurally mimic HBGAs. These results suggest that 2'FL and 3FL might act as naturally occurring decoys in humans.

Organizational Affiliation

Pediatric Infectious Diseases Unit, University Children's Hospital Mannheim, University of Heidelberg, Mannheim, Germany.

Macromolecule Content

Total Structure Weight: 70.18 kDa
Atom Count: 5,750
Modeled Residue Count: 621
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	315	Norovirus GII.10	Mutation(s): 0
UniProt
Find proteins for Q5F4T5 (Norwalk virus) Explore Q5F4T5 Go to UniProtKB: Q5F4T5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5F4T5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G57548NB GlyCosmos: G57548NB GlyGen: G57548NB

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 D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.179 (Depositor), 0.179 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.71	α = 90
b = 78.17	β = 102.3
c = 71.84	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Hansman, G.S.

Koromyslova, A.D.

Singh, B.K.

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-04-27
Changes: Database references
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