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- PDB-6r0f: Getah virus macro domain in complex with ADPr, pose 1 -

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Basic information

Entry
Database: PDB / ID: 6r0f
TitleGetah virus macro domain in complex with ADPr, pose 1
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 / ribonucleoside triphosphate phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / 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
Chem-AR6 / Polyprotein P1234 / Polyprotein P1234
Similarity search - Component
Biological speciesGetah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsSulzenbacher, G. / Ferreira Ramos, A.S. / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)37,3604
Polymers36,2412
Non-polymers1,1192
Water3,315184
1
A: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6802
Polymers18,1211
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6802
Polymers18,1211
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.729, 71.566, 98.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 1 - 160 / Label seq-ID: 3 - 162

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A143SL92, UniProt: Q5Y389*PLUS
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: imidazole-Malate pH 5,9 34% PEG 4K, 3mM ADPr, 3 hours soaking with crystallization solutution additioned 15mM Aspartic acid,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→42.23 Å / Num. obs: 21125 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.097 / Rrim(I) all: 0.16 / Rsym value: 0.27 / Net I/σ(I): 8.5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1628 / CC1/2: 0.468 / Rpim(I) all: 0.908 / Rrim(I) all: 1.517 / Rsym value: 1.206 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QZU

6qzu


Resolution: 2.05→40.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.923 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23548 1238 5.9 %RANDOM
Rwork0.19273 ---
obs0.19514 19838 98.27 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2---1.52 Å20 Å2
3---4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 72 184 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132500
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172332
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.6893400
X-RAY DIFFRACTIONr_angle_other_deg1.3341.6065384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80220.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9415402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8121522
X-RAY DIFFRACTIONr_chiral_restr0.0590.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
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_it2.1233.5351278
X-RAY DIFFRACTIONr_mcbond_other2.1173.5311277
X-RAY DIFFRACTIONr_mcangle_it3.2465.2841594
X-RAY DIFFRACTIONr_mcangle_other3.2455.2881595
X-RAY DIFFRACTIONr_scbond_it2.7774.091222
X-RAY DIFFRACTIONr_scbond_other2.7754.0911223
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4945.9531807
X-RAY DIFFRACTIONr_long_range_B_refined6.53343.42830
X-RAY DIFFRACTIONr_long_range_B_other6.48143.232786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4926 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 96 -
Rwork0.316 1452 -
obs--98.79 %

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