[English] 日本語
Yorodumi
- PDB-8u1v: Structure of Norovirus (Hu/GII.4/Sydney/NSW0514/2012/AU) protease... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u1v
TitleStructure of Norovirus (Hu/GII.4/Sydney/NSW0514/2012/AU) protease in the ligand-free state
ComponentsPeptidase C37
KeywordsVIRAL PROTEIN / Protease / 3-chymotrypsin-like protease / 3CL-pro
Function / homology
Function and homology information


host cell membrane / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / ATP 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsEruera, A.R. / Campbell, A.C. / Krause, K.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)UOOX1904 New Zealand
CitationJournal: Viruses / Year: 2023
Title: Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease.
Authors: Eruera, A.R. / McSweeney, A.M. / McKenzie-Goldsmith, G.M. / Opel-Reading, H.K. / Thomas, S.X. / Campbell, A.C. / Stubbing, L. / Siow, A. / Hubert, J.G. / Brimble, M.A. / Ward, V.K. / Krause, K.L.
History
DepositionSep 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidase C37
B: Peptidase C37
C: Peptidase C37
D: Peptidase C37


Theoretical massNumber of molelcules
Total (without water)77,3214
Polymers77,3214
Non-polymers00
Water1629
1
A: Peptidase C37
B: Peptidase C37


Theoretical massNumber of molelcules
Total (without water)38,6612
Polymers38,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area15810 Å2
MethodPISA
2
C: Peptidase C37
D: Peptidase C37


Theoretical massNumber of molelcules
Total (without water)38,6612
Polymers38,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.827, 160.869, 95.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

-
Components

#1: Protein
Peptidase C37


Mass: 19330.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Production host: Escherichia coli (E. coli)
References: UniProt: K4L8Z7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% w/v PEG 3350, 8% Tacsimate pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.79→48.54 Å / Num. obs: 21735 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.097 / Rrim(I) all: 0.184 / Net I/σ(I): 7.1
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.257 / Mean I/σ(I) obs: 1 / Num. unique obs: 2936 / CC1/2: 0.512 / Rpim(I) all: 0.777 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→48.54 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 647 3 %Random selection
Rwork0.1942 ---
obs0.1948 21581 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 0 9 5015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025128
X-RAY DIFFRACTIONf_angle_d0.4836987
X-RAY DIFFRACTIONf_dihedral_angle_d12.9611772
X-RAY DIFFRACTIONf_chiral_restr0.044809
X-RAY DIFFRACTIONf_plane_restr0.005892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-3.010.34141190.29683847X-RAY DIFFRACTION92
3.01-3.310.28161300.25044212X-RAY DIFFRACTION100
3.31-3.790.21461310.20154223X-RAY DIFFRACTION100
3.79-4.770.16781320.16264254X-RAY DIFFRACTION100
4.77-48.540.20581350.17684398X-RAY DIFFRACTION100
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)
10.6739-0.25870.36210.5320.04410.2850.06310.04660.00110.054-0.0531-0.08350.0709-0.040900.36330.0096-0.02150.3144-0.01280.292215.04910.35149.2668
21.1365-0.1303-0.12820.3511-0.27280.2874-0.07670.09490.22960.07970.0337-0.14330.1098-0.0756-00.3145-0.0412-0.01860.3710.0580.331910.798334.4766-12.0871
30.1887-0.35930.02460.6983-0.07930.18660.0927-0.0251-0.0420.05750.06640.11210.05770.0281-00.4252-0.01320.02210.41020.00590.4048-21.604512.21699.9942
40.62340.0368-0.0470.6764-0.34490.3371-0.0062-0.09690.1353-0.06330.10990.0251-0.05990.118200.28170.0405-0.04170.2488-0.03020.3798-15.746243.119412.623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 181)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 175)
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 172)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 172)

+
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