[English] 日本語
Yorodumi
- PDB-8p0e: Rubella virus p150 macro domain in complex with ADP-ribose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p0e
TitleRubella virus p150 macro domain in complex with ADP-ribose
ComponentsNon-structural polyprotein p200
KeywordsHYDROLASE / Macro domain / A1pp domain / ADP-ribosylhydrolase / ADP-ribose
Function / homology
Function and homology information


mRNA methyltransferase activity / host cell membrane / RNA processing / ribonucleoside triphosphate phosphatase activity / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...mRNA methyltransferase activity / host cell membrane / RNA processing / ribonucleoside triphosphate phosphatase activity / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
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 ...: / 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
ADENOSINE-5-DIPHOSPHORIBOSE / Non-structural polyprotein p200
Similarity search - Component
Biological speciesRubella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsStoll, G.A. / Modis, Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S021604/1 United Kingdom
Wellcome Trust217191/Z/19/Z United Kingdom
Wellcome Trust205833/Z/16/Z United Kingdom
Citation
Journal: J.Virol. / Year: 2024
Title: Crystal structure and biochemical activity of the macrodomain from rubella virus p150.
Authors: Stoll, G.A. / Nikolopoulos, N. / Zhai, H. / Zhang, L. / Douse, C.H. / Modis, Y.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: 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 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural polyprotein p200
B: Non-structural polyprotein p200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0204
Polymers39,9022
Non-polymers1,1192
Water6,251347
1
A: Non-structural polyprotein p200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5102
Polymers19,9511
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural polyprotein p200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5102
Polymers19,9511
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.830, 87.450, 135.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

-
Components

#1: Protein Non-structural polyprotein p200


Mass: 19950.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus / Gene: NSP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G3M8F4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.54 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 14.4% PEG 6K, 1.26 M LiCl, 0.1 M Bicine pH 9, supplemented with 10% glycerol for freezing

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 9, 2020 / Details: Focussing mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.59→73.5 Å / Num. obs: 31161 / % possible obs: 91.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.033 / Net I/σ(I): 12.8
Reflection shellResolution: 1.594→1.774 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7965 / CC1/2: 0.621 / Rpim(I) all: 0.454 / % possible all: 68.7

-
Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
autoPROC1.0.5data reduction
STARANISO1.0.4data scaling
PHASERphasing
autoPROC1.0.5data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→67.92 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2061 1569 5.04 %
Rwork0.1919 29590 -
obs0.1926 31159 53.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.61 Å2
Refinement stepCycle: LAST / Resolution: 1.59→67.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 72 347 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01932859
X-RAY DIFFRACTIONf_angle_d0.84593930
X-RAY DIFFRACTIONf_chiral_restr0.0465454
X-RAY DIFFRACTIONf_plane_restr0.0168510
X-RAY DIFFRACTIONf_dihedral_angle_d7.0675419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.650.439390.4026176X-RAY DIFFRACTION3.53
1.65-1.70.392270.3174511X-RAY DIFFRACTION10.32
1.7-1.770.347390.3086779X-RAY DIFFRACTION15.69
1.77-1.850.2827660.25881227X-RAY DIFFRACTION24.79
1.85-1.950.26781050.26332158X-RAY DIFFRACTION43.2
1.95-2.070.23541570.22942835X-RAY DIFFRACTION56.93
2.07-2.230.2391650.223375X-RAY DIFFRACTION67.33
2.23-2.460.24792350.21113973X-RAY DIFFRACTION79.59
2.46-2.810.23182560.20474755X-RAY DIFFRACTION94.65
2.81-3.540.21052590.18374892X-RAY DIFFRACTION96.3
3.55-67.920.16012510.16444909X-RAY DIFFRACTION93.28
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)
12.74842545237-1.01866122047-0.3008031783951.810867453850.2807789265972.258553135020.0457620174639-0.170709593195-0.510221703126-0.188937550029-0.06192095771890.2124978927170.4171517272650.08633266245640.0356096658660.2141272177450.005682890830760.006826739765780.1979997648630.01185379831040.23476794296613.125246795114.767225599752.5144334687
23.179335374690.2822781436510.2735973907930.5371837651470.3806237341983.056295380560.0858100205774-0.426207815648-0.4551008428090.0716106321685-0.101255809637-0.1398678262810.479618353190.823788527212-0.1012331719980.2606373229860.10102107372-0.01994237870230.4562908422980.01686758707940.27707183318133.352600319513.863488957257.6502278092
32.327316972830.07440894560850.007666489915882.75031212099-0.6709980793693.19838487394-0.0801953695168-1.084025216590.3708909059450.507071542431-0.00839574126943-0.202604319974-0.6364124772830.207807686811-0.2453502319350.3309092188670.032181321115-0.08619873866170.606085854252-0.1905885738150.19146788244426.926546054724.390122770564.8422968043
44.19692455564-0.944774273842-0.2157745913161.18634524794-0.110697859193.25838517343-0.0226724942309-0.5240249255310.2835403825170.0004106524019170.024915221106-0.143628638468-0.1961573301170.180788613075-0.1498215932480.172414149502-0.005615903989820.0008752003378740.208363777042-0.03454001360580.18912647461220.747992850424.403166848456.1826504581
54.9970838145-1.35362043531-0.7108997136242.788423747070.450291790124.421182068020.111374772598-0.1947626829360.2731626808730.55023571448-0.377466032093-0.638354530528-0.2618990433320.130756086376-0.05255775768760.1978986949240.0270977558110.02355871255110.5282592015190.04946995072710.1942103114036.2592087313323.668534260464.3378157236
62.025750885160.600837197256-0.5196397194222.23707584148-0.8504409418012.50995411365-0.04757744365350.0994289849329-0.2562852981950.1424393732150.179491784728-0.1021521245770.1463544270980.182432055034-0.02747651812510.1802200536880.008973787644440.01609099336560.146322457916-0.0454261556720.20437533572137.35366410129.6270483811121.2839521115
73.017712747660.750901389239-0.5195245614860.9949800746830.2452860880492.944870217650.04671360110110.0135666826243-0.1519472887050.09813786519340.04291580307750.3434939845230.117579629938-0.693866033391-0.001496440652270.210367704133-0.003260181169090.03613374061990.3028945267090.03872149949330.27861076963618.788572849711.386894356829.1232011423
82.118703609660.8323066342640.5398048587771.08593164560.09970859403563.429990851080.01134559252510.04206897909210.1224773151330.05271003277220.1323672739190.1857711605-0.332801014273-0.249156430705-0.08611093955880.2096011071390.0331202995560.05984537396340.1765494540530.02062656755050.19735287828425.422648796120.104210914323.136353885
93.793573919191.083792814040.8763967159162.381080687032.098030895294.254156406990.03982438028470.5946849581560.34587912271-0.1123176211420.06012919130210.1503588149-0.5196700997450.165582404457-0.06451274575030.264943990825-0.002731456741990.04046701016070.1852270564940.03108666255020.178296841930.925812666522.024045068616.4266878354
102.38535527548-0.915963758399-0.7468373876331.24750097745-0.428950772472.64804494474-0.05380864173990.00349320385127-0.0247941702047-0.1157261735380.327946391567-0.19398900004-0.4781196446870.197860718814-0.1260656167840.233296710462-0.01798570570120.05085065634460.106920230276-0.01480245264490.17784858665634.93064019916.129010786224.7869527732
115.240995817040.138775214432-0.8454407539422.24183900518-1.053558956235.48230624170.1309044498490.5291582418190.274528178894-0.0916938629393-0.06637601538730.426571017895-0.2392003234110.102082535399-0.1562956651150.2097223836-0.02231687183620.003610357337140.384039458303-0.01251464379650.17324860212334.191210616418.08735579826.88491302675
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 32 )AA3 - 321 - 30
22chain 'A' and (resid 33 through 86 )AA33 - 8631 - 84
33chain 'A' and (resid 87 through 101 )AA87 - 10185 - 99
44chain 'A' and (resid 102 through 170 )AA102 - 170100 - 168
55chain 'A' and (resid 171 through 186 )AA171 - 186169 - 184
66chain 'B' and (resid 2 through 32 )BC2 - 321 - 31
77chain 'B' and (resid 33 through 99 )BC33 - 9932 - 98
88chain 'B' and (resid 100 through 142 )BC100 - 14299 - 141
99chain 'B' and (resid 143 through 155 )BC143 - 155142 - 154
1010chain 'B' and (resid 156 through 170 )BC156 - 170155 - 169
1111chain 'B' and (resid 171 through 187 )BC171 - 187170 - 186

+
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