3SFU

crystal structure of murine norovirus RNA dependent RNA polymerase in complex with ribavirin

PDB DOI: https://doi.org/10.2210/pdb3SFU/pdb

Classification: TRANSFERASE
Organism(s): Murine norovirus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-14 Released: 2012-05-09
Deposition Author(s): Kim, K.H., Alam, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.229
R-Value Work: 0.181
R-Value Observed: 0.182

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-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin.

Alam, I., Lee, J.H., Cho, K.J., Han, K.R., Yang, J.M., Chung, M.S., Kim, K.H.

(2012) Virology 426: 143-151

PubMed: 22341781 Search on PubMed
DOI: https://doi.org/10.1016/j.virol.2012.01.016
Primary Citation of Related Structures:
3SFG, 3SFU

PubMed Abstract:
Murine norovirus-1 (MNV-1) shares many features with human norovirus (HuNoV) and both are classified within the norovirus genus of Caliciviridae family. MNV-1 is used as the surrogate for HuNoV research since it is the only form that can be grown in cell culture. HuNoV and MNV-1 RNA dependent RNA polymerase (RdRp) proteins with the sequence identity of 59% show essentially identical conformations. Here we report the first structural evidence of 2-thiouridine (2TU) or ribavirin binding to MNV-1 RdRp, based on the crystal structures determined at 2.2? and 2.5? resolutions, respectively. Cellular and biochemical studies revealed stronger inhibitory effect of 2TU on the replication of MNV-1 in RAW 264.7 cells, compared to that of ribavirin. Our complex structures highlight the key interactions involved in recognition of the nucleoside analogs which block the active site of the viral RNA polymerase.

Organizational Affiliation

Department of Biotechnology & Bioinformatics, Korea University, Chungnam 339-700, Republic of Korea.

Macromolecule Content

Total Structure Weight: 181.35 kDa
Atom Count: 12,321
Modelled Residue Count: 1,445
Deposited Residue Count: 1,551
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase	A, B, C	517	Murine norovirus 1	Mutation(s): 0 Gene Names: RdRp
UniProt
Find proteins for Q80J95 (Norovirus (isolate Mouse/NoV/United States/MNV1/2002/GV)) Explore Q80J95 Go to UniProtKB: Q80J95
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q80J95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RBV Query on RBV Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain PA [auth C] SDF format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain X [auth B]	D [auth A], PA [auth C], X [auth B]	1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide C₈ H₁₂ N₄ O₅ IWUCXVSUMQZMFG-AFCXAGJDSA-N		Interactions Focus chain D [auth A] Focus chain PA [auth C] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain PA [auth C] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth B] 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 A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain TA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] 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 A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] 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 A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Y [auth B]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], E [auth A], EA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], QA [auth C], RA [auth C], TA [auth C], VA [auth C], WA [auth C], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	EB [auth C] FB [auth C] GA [auth B] GB [auth C] HA [auth B] EB [auth C], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], LA [auth B], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], UA [auth C], V [auth A], W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain W [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain M [auth A] SDF format, chain SA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain SA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain SA [auth C]	FA [auth B], M [auth A], SA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain M [auth A] Focus chain SA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain M [auth A] Focus chain SA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.229
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 119.952	α = 90
b = 196.084	β = 114.12
c = 109.206	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Kim, K.H.

Alam, I.

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary