[English] 日本語
Yorodumi
- PDB-7fav: Crystal Structure of Rubella Protease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fav
TitleCrystal Structure of Rubella Protease
ComponentsProtease/methyltransferase p150
KeywordsHYDROLASE / Viral protease / VIRAL PROTEIN
Function / homology
Function and homology information


mRNA methyltransferase activity / host cell membrane / RNA processing / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication ...mRNA methyltransferase activity / host cell membrane / RNA processing / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Peptidase C27, rubella virus endopeptidase / Rubivirus non-structural protein, C-terminal / Rubella virus (RUBV) nonstructural (NS) protease domain / Rubella virus endopeptidase / Rubivirus non-structural protein / Rubella virus (RUBV) nonstructural (NS) protease domain profile. / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase ...Peptidase C27, rubella virus endopeptidase / Rubivirus non-structural protein, C-terminal / Rubella virus (RUBV) nonstructural (NS) protease domain / Rubella virus endopeptidase / Rubivirus non-structural protein / Rubella virus (RUBV) nonstructural (NS) protease domain profile. / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Non-structural polyprotein p200
Similarity search - Component
Biological speciesRubella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsQuek, J.P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF2016NRF-CRP001-063 Singapore
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure of the Rubella virus protease reveals a unique papain-like protease fold.
Authors: Cheong, E.Z.K. / Quek, J.P. / Xin, L. / Li, C. / Chan, J.Y. / Liew, C.W. / Mu, Y. / Zheng, J. / Luo, D.
History
DepositionJul 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease/methyltransferase p150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,10011
Polymers30,3241
Non-polymers77610
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint18 kcal/mol
Surface area12400 Å2
Unit cell
Length a, b, c (Å)60.243, 60.243, 173.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Protease/methyltransferase p150 / p150


Mass: 30324.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus (strain RA27/3 vaccine) / Strain: RA27/3 vaccine / Production host: Escherichia coli (E. coli)
References: UniProt: O40955, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

-
Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 12.5% Peg 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.28482 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28482 Å / Relative weight: 1
ReflectionResolution: 1.64→41.37 Å / Num. obs: 40150 / % possible obs: 99.7 % / Redundancy: 51 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.012 / Rrim(I) all: 0.087 / Net I/σ(I): 41.82
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 49.8 % / Rmerge(I) obs: 1.09 / Num. unique obs: 3811 / CC1/2: 0.912 / Rpim(I) all: 0.1525 / % possible all: 96.87

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→41.37 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / Phase error: 16.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1988 2075 5.2 %
Rwork0.1801 38076 -
obs-40150 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.26 Å2 / Biso min: 15.87 Å2
Refinement stepCycle: final / Resolution: 1.64→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 88 172 2292
Biso mean--49.41 41.13 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.6980.20831850.2163362695
2.0223-2.11430.19481320.17772519100
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)
13.0337-1.25880.74173.507-0.56471.5280.05020.0485-0.1424-0.1322-0.01640.0460.15040.0589-0.03660.20480.04290.02480.21160.02570.203237.19980.499230.2994
22.2761-0.159-1.05047.47462.53853.83410.0929-0.00860.158-0.13880.0809-0.1539-0.18790.0837-0.1970.13150.0507-0.03740.19360.06760.178436.48238.149732.0465
35.6984-5.8828-3.26047.63152.68315.3777-0.3238-0.4135-0.05970.17340.203-0.27430.2110.36580.13640.18750.0458-0.05030.3023-0.00340.131236.93046.29145.6064
42.4384-0.6133-0.27790.7653-0.17291.78150.0099-0.0314-0.10340.05430.00990.01770.15910.0437-0.04790.21240.03350.01510.17360.02370.232318.56876.694639.2995
57.8557-6.53110.267.4012-1.14773.00110.04390.0449-0.62630.02340.08460.56480.1328-0.2851-0.10170.1995-0.034-0.01750.24470.00930.25197.32121.636231.0518
62.1028-0.1516-0.30150.12250.09371.69790.03640.07790.2763-0.02090.03160.0432-0.17650.0099-0.04280.23780.04260.01720.17190.03250.268116.051217.624235.7934
73.2177-0.5417-2.73051.8818-0.9246.94310.05020.13130.33850.05160.1122-0.05160.0254-0.0939-0.10360.20130.01090.01270.15930.01110.283125.338719.968132.7233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1031 through 1083 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1084 through 1103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1104 through 1123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1124 through 1189 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1190 through 1203 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1204 through 1278 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1279 through 1299 )

+
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://pdbjlvh1.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