6H6L

Murine norovirus protruding domain (CW3 strain) in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)

PDB DOI: https://doi.org/10.2210/pdb6H6L/pdb

Classification: VIRAL PROTEIN
Organism(s): Murine norovirus 1, Mus musculus
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2018-07-27 Released: 2019-08-14
Deposition Author(s): Kilic, T., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.216
R-Value Work: 0.189
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of murine norovirus protruding domain with conjugated bile acid reveal a novel binding pocket.

Kilic, T., Koromyslova, A., Malak, V., Hansman, G.S.

To be published.

Macromolecule Content

Total Structure Weight: 185.02 kDa
Atom Count: 12,309
Modelled Residue Count: 1,624
Deposited Residue Count: 1,660
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D	303	Murine norovirus 1	Mutation(s): 0
UniProt
Find proteins for A7U694 (Norovirus (isolate Mouse/NoV/United States/MNV1/2002/GV)) Explore A7U694 Go to UniProtKB: A7U694
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7U694
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CMRF35-like molecule 1	E, F, G, H	112	Mus musculus	Mutation(s): 0 Gene Names: Cd300lf, Clm1, Lmir3
UniProt
Find proteins for Q6SJQ7 (Mus musculus) Explore Q6SJQ7 Go to UniProtKB: Q6SJQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6SJQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHO Query on CHO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D]	K [auth A], M [auth B], T [auth C], V [auth D]	GLYCOCHENODEOXYCHOLIC ACID C₂₆ H₄₃ N O₅ GHCZAUBVMUEKKP-GYPHWSFCSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain V [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain V [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	I [auth A] J [auth A] N [auth B] O [auth B] R [auth C] I [auth A], J [auth A], N [auth B], O [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	L [auth A], Q [auth B], U [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.216
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87	α = 90
b = 87	β = 90
c = 276.81	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Kilic, T.

Hansman, G.S.

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description