[English] 日本語
Yorodumi
- PDB-4x2w: Crystal structure of the Murine Norovirus NS6 protease (inactive ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x2w
TitleCrystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residues P1 prime - P2 prime of NS7
ComponentsNS6 Protease
KeywordsHYDROLASE / Murine norovirus Protease
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFernandes, H. / Leen, E.N. / Curry, S.
Citation
Journal: Peerj / Year: 2015
Title: Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions.
Authors: Fernandes, H. / Leen, E.N. / Cromwell, H. / Pfeil, M.P. / Curry, S.
#1: Journal: PLoS ONE / Year: 2012
Title: Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation.
Authors: Leen, E.N. / Baeza, G. / Curry, S.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS6 Protease
B: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)37,5612
Polymers37,5612
Non-polymers00
Water0
1
A: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,7811
Polymers18,7811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,7811
Polymers18,7811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.940, 135.940, 82.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 4 - 181 / Label seq-ID: 2 - 179

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein NS6 Protease


Mass: 18780.504 Da / Num. of mol.: 2 / Fragment: UNP residues 997-1175 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q80J95

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% (v/v) PEG 3350, 0.1 M glycine, 0.1 M Na-citrate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→117.85 Å / Num. obs: 8555 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ASH

4ash


Resolution: 2.7→117.85 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.863 / SU B: 67.36 / SU ML: 0.534 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 469 4.9 %Random selection
Rwork0.2536 9071 --
obs0.256 8555 74.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.26 Å2 / Biso mean: 87.171 Å2 / Biso min: 42.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----3.21 Å2
Refinement stepCycle: final / Resolution: 2.7→117.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 0 2562
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192622
X-RAY DIFFRACTIONr_bond_other_d0.0050.022520
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9373565
X-RAY DIFFRACTIONr_angle_other_deg1.12935785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.675342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31722.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73115400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212958
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02594
X-RAY DIFFRACTIONr_mcbond_it1.1782.4651379
X-RAY DIFFRACTIONr_mcbond_other1.1782.4641378
X-RAY DIFFRACTIONr_mcangle_it2.1663.6881718
Refine LS restraints NCS

Ens-ID: 1 / Number: 8802 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 11 -
Rwork0.395 139 -
all-150 -
obs--16.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.41181.3608-0.67245.8139-0.14967.8662-0.3530.1345-0.01390.18250.1922-0.26960.5666-0.39470.16080.6323-0.1315-0.08490.0463-0.0090.3524-9.292695.097387.4157
24.1189-0.49092.04577.6535-0.19247.97470.08410.4669-0.01650.03550.08260.7932-0.5622-1.0079-0.16670.8080.21410.03570.28980.06640.6194-22.0722114.9208107.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 181
2X-RAY DIFFRACTION2B4 - 181

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more