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- PDB-6qzu: Getah virus macro domain -

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Basic information

Entry
Database: PDB / ID: 6qzu
TitleGetah virus macro domain
ComponentsNon-structural polyprotein
KeywordsVIRAL PROTEIN / Macro domain / Getah virus
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell nucleus / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase ...: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / 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 core domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Polyprotein P1234 / Polyprotein P1234
Similarity search - Component
Biological speciesGetah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFerreira Ramos, A.S. / Sulzenbacher, G. / Coutard, B.
CitationJournal: Sci Rep / Year: 2020
Title: Snapshots of ADP-ribose bound to Getah virus macro domain reveal an intriguing choreography.
Authors: Ferreira-Ramos, A.S. / Sulzenbacher, G. / Canard, B. / Coutard, B.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,4094
Polymers36,2412
Non-polymers1682
Water3,423190
1
A: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2272
Polymers18,1211
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1832
Polymers18,1211
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.552, 71.358, 94.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural polyprotein / Macro domain


Mass: 18120.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic gene / Source: (gene. exp.) Getah virus / Gene: nsP1234 / Plasmid: pDest14
Details (production host): from ThermoFischer, Gateway cloning
Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLysS / References: UniProt: A0A143SL92, UniProt: Q5Y389*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0,2M Imidazole Malate pH6 30% PEG 4K / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 2→41.8 Å / Num. all: 99003 / Num. obs: 22033 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.108 / Rrim(I) all: 0.173 / Rsym value: 0.134 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6918 / CC1/2: 0.603 / Rpim(I) all: 0.619 / Rrim(I) all: 0.976 / Rsym value: 0.748 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GPG

3gpg


Resolution: 2→41.8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.751 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23108 1278 5.8 %RANDOM
Rwork0.19386 ---
obs0.196 20700 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.891 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å2-0 Å2-0 Å2
2---0.38 Å2-0 Å2
3---3.8 Å2
Refinement stepCycle: 1 / Resolution: 2→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 11 190 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192469
X-RAY DIFFRACTIONr_bond_other_d0.0020.022403
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9423351
X-RAY DIFFRACTIONr_angle_other_deg0.89935517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41923.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70815412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3571522
X-RAY DIFFRACTIONr_chiral_restr0.070.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5251.1351292
X-RAY DIFFRACTIONr_mcbond_other0.5241.1341291
X-RAY DIFFRACTIONr_mcangle_it0.9361.6951615
X-RAY DIFFRACTIONr_mcangle_other0.9361.6971616
X-RAY DIFFRACTIONr_scbond_it0.5661.2961177
X-RAY DIFFRACTIONr_scbond_other0.5631.2961177
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9711.881730
X-RAY DIFFRACTIONr_long_range_B_refined4.72214.6822767
X-RAY DIFFRACTIONr_long_range_B_other4.614.1182722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 91 -
Rwork0.277 1504 -
obs--99.69 %
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)
11.6642-0.6274-0.08911.53370.19561.29190.0420.19650.0492-0.0927-0.0338-0.0825-0.02620.0061-0.00820.176-0.01250.00780.13930.02670.0094-0.874723.6597-10.9224
22.29150.2701-0.07142.4537-0.19491.19780.0377-0.40270.02250.2818-0.06130.0212-0.09550.01040.02360.2051-0.0050.01730.1940.00270.00290.34749.241811.5671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 160
2X-RAY DIFFRACTION2B1 - 160

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