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- PDB-8p0c: Rubella virus p150 macro domain (apo) -

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Basic information

Entry
Database: PDB / ID: 8p0c
TitleRubella virus p150 macro domain (apo)
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
Non-structural polyprotein p200
Similarity search - Component
Biological speciesRubella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
CitationJournal: 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.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,9022
Polymers39,9022
Non-polymers00
Water6,035335
1
A: Non-structural polyprotein p200


Theoretical massNumber of molelcules
Total (without water)19,9511
Polymers19,9511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural polyprotein p200


Theoretical massNumber of molelcules
Total (without water)19,9511
Polymers19,9511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.682, 87.569, 135.507
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
11A-224-

HOH

21B-328-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.5 % / 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 prior to freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2020 / Details: Focussing mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.72→64.1 Å / Num. obs: 23298 / % possible obs: 91.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 21.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 1.723→1.949 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1165 / CC1/2: 0.613 / Rpim(I) all: 0.514 / % possible all: 53.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
STARANISO1.0.4data scaling
Cootmodel building
autoPROC1.0.5data reduction
autoPROC1.0.5data processing
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→43 Å / SU ML: 0.1684 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 1183 5.08 %
Rwork0.1862 22111 -
obs0.1883 23294 50.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.94 Å2
Refinement stepCycle: LAST / Resolution: 1.72→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 335 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522781
X-RAY DIFFRACTIONf_angle_d0.81813810
X-RAY DIFFRACTIONf_chiral_restr0.0461438
X-RAY DIFFRACTIONf_plane_restr0.0162508
X-RAY DIFFRACTIONf_dihedral_angle_d5.7651413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.80.09420.295152X-RAY DIFFRACTION0.95
1.8-1.90.3508260.2833505X-RAY DIFFRACTION9.42
1.9-2.020.3294800.25431499X-RAY DIFFRACTION27.7
2.02-2.170.27381320.22542530X-RAY DIFFRACTION46.75
2.17-2.390.23171690.21652937X-RAY DIFFRACTION54.09
2.39-2.740.23751880.21373872X-RAY DIFFRACTION70.84
2.74-3.450.23412800.18675060X-RAY DIFFRACTION92.1
3.45-430.20693060.16235656X-RAY DIFFRACTION99.53
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)
13.71718880591-1.84515147935-0.2112760779313.50574707647-0.1001991299763.02187929018-0.0637783704835-0.212732624031-0.485625620297-0.2815811637540.06024432935220.1993879903120.471085442951-0.1748070645160.02121692380080.162440610472-0.0230722672124-0.001442123960410.186338209253-0.006306794083970.17832773846113.033035061214.792000412752.4090895436
24.166939054510.4575146540790.6605791121250.5128760263850.1155605432463.377954440630.0138558310122-0.24408286521-0.4184933425340.06933774648110.0391643713786-0.1394219217620.4607380742841.09513197313-0.01364955345270.2352325935980.08667609034840.005767309290390.4463821834720.01054760972830.23614629651433.241298371413.763428176157.5848506937
32.093746388330.399556625812-0.1776116153463.03856533867-0.6575614189323.11820676268-0.296675818267-0.6887009516190.5844777150310.499811464566-0.205711829965-0.151727770378-0.8668654368420.394389701351-0.06246135829010.325829385520.0834474250255-0.1327670765330.48746794511-0.1773601854170.24610704830126.874524895724.335646179764.7413561763
44.00333497764-0.952980274978-0.3626183673351.8996093063-0.4240518370334.28780510363-0.042343212083-0.4063792022370.2863686164130.05101340841960.00900520811673-0.116453224293-0.2782045194620.3045918996190.001126918937510.105815905523-0.009447606049250.003969118634150.176175091582-0.02828872971610.15290535151520.725551082824.361142330256.1111360689
56.05747544538-4.20265503882-0.9847791918713.23638169753-0.1052751027035.213445872520.10501655524-0.3016461495040.07115596561550.16362135617-0.178929051119-0.206279764634-0.3342653048920.04211318465780.2973002614890.1831025920560.01203309130530.02117518319130.3979519260380.03286919935740.1923444624216.1896518870923.77620128264.2086711854
62.466192895941.08461228881-0.633009070793.73290985433-1.028631886543.29844818146-0.105959176080.0108336447183-0.259971844930.06484367527630.148988660237-0.1951794707890.1730160682470.153533808862-0.1158477031380.1008646676640.01202217670020.004472985615740.123338023765-0.03657229440070.16861480380837.36889317759.592779454321.2484019198
72.699065540940.5437271629370.2834905327631.6192153811-0.5766775782173.737102929050.0652631671216-0.0952483271516-0.3411829503220.04857894917490.1197542577280.5764159935740.358612773864-0.912624748512-0.1437415283940.253904691874-0.01545965072440.04014180964060.3874121755710.04133363368320.30076472885618.702327428911.256272150429.0180068518
82.665391362670.3694080250711.673207684561.35688097346-0.8030941791525.28479722159-0.125431512339-0.1382094925840.1372859485530.06524088750820.2061292695250.144675103519-0.272634589464-0.367710589223-0.1073801381030.147333221680.02454058322750.04791269540840.1291763500140.002007055328560.13683146587525.325171635819.997042836523.0918346316
96.013823987671.489032947082.400777006742.986888446642.788372240826.90373499598-0.1429948789830.6398809997350.5852791940080.05948554427340.1825225159830.233812184231-0.4921980990820.420900603005-0.05833132014210.191328604047-0.02118995084660.03268312401960.130916096940.01386654426090.16999750058730.862936254921.924533726916.3670120134
102.7018445444-1.41528088151-0.9098533706371.13849256675-0.6475773715053.49837122698-0.136623421948-0.1573429097070.0395986028783-0.01716225900520.427674168378-0.333292647891-0.4200313612330.515702300861-0.2749729861180.189834936897-0.006578047168970.05498673487910.125349887482-0.001859351443530.13133429899934.821964706516.074055377124.7425410414
116.099851613270.722637960802-1.043109533276.75743960725-3.245038964457.054467505690.27910369920.2864977569160.2757458875050.108585453814-0.3301401384410.265562178499-0.30739687472-0.227257025731-0.06309599694390.146575025957-0.0004749168651610.0166134288080.296934720793-0.03225530017850.1391041364434.17925416518.02480067996.83856545914
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 )BB2 - 321 - 31
77chain 'B' and (resid 33 through 99 )BB33 - 9932 - 98
88chain 'B' and (resid 100 through 142 )BB100 - 14299 - 141
99chain 'B' and (resid 143 through 155 )BB143 - 155142 - 154
1010chain 'B' and (resid 156 through 170 )BB156 - 170155 - 169
1111chain 'B' and (resid 171 through 187 )BB171 - 187170 - 186

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