6H6M | pdb_00006h6m

CR10 murine norovirus protruding domain in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)

PDB DOI: https://doi.org/10.2210/pdb6H6M/pdb

Classification: VIRAL PROTEIN
Organism(s): Murine norovirus GV/CR10/2005/USA, 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: 2.38 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.186 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 160.74 kDa
Atom Count: 11,579
Modeled Residue Count: 1,434
Deposited Residue Count: 1,434
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D	303	Murine norovirus GV/CR10/2005/USA	Mutation(s): 0
UniProt
Find proteins for A7YK37 (Murine norovirus GV/CR10/2005/USA) Explore A7YK37 Go to UniProtKB: A7YK37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7YK37
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CMRF35-like molecule 1	E, F	111	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6SJQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHO Query on CHO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	G [auth A], M [auth B], S [auth C], X [auth D]	GLYCOCHENODEOXYCHOLIC ACID C₂₆ H₄₃ N O₅ GHCZAUBVMUEKKP-GYPHWSFCSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] MOL2 format, chain EA [auth F] mmCIF format, chain EA [auth F]	EA [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Interactions & Density Focus chain EA [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] MOL2 format, chain CA [auth E] mmCIF format, chain CA [auth E]	CA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Interactions & Density Focus chain CA [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth E] DA [auth F] H [auth A] I [auth A] AA [auth D], BA [auth E], DA [auth F], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth D] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D]	L [auth A], N [auth B], W [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain L [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.186 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.94	α = 90
b = 137.55	β = 95.84
c = 93.8	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

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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
Version 1.2: 2024-10-16
Changes: Structure summary