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- PDB-3gqo: Crystal structure of macro domain of Venezuelan Equine Encephalit... -

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Basic information

Entry
Database: PDB / ID: 3gqo
TitleCrystal structure of macro domain of Venezuelan Equine Encephalitis virus in complex with ADP-ribose
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / macro domain / X domain / Venezuelan Equine Encephalitis virus / alphavirus / virus / ADP-ribose / VIZIER / Viral enzymes involved in replication
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 / 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
ADENOSINE-5-DIPHOSPHORIBOSE / Polyprotein P1234
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMalet, H. / Jamal, S. / Coutard, B. / Ferron, F. / Canard, B.
CitationJournal: J.Virol. / Year: 2009
Title: The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket
Authors: Malet, H. / Coutard, B. / Jamal, S. / Dutartre, H. / Papageorgiou, N. / Neuvonen, M. / Ahola, T. / Forrester, N. / Gould, E.A. / Lafitte, D. / Ferron, F. / Lescar, J. / Gorbalenya, A.E. / de ...Authors: Malet, H. / Coutard, B. / Jamal, S. / Dutartre, H. / Papageorgiou, N. / Neuvonen, M. / Ahola, T. / Forrester, N. / Gould, E.A. / Lafitte, D. / Ferron, F. / Lescar, J. / Gorbalenya, A.E. / de Lamballerie, X. / Canard, B.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 20, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.detector
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6978
Polymers73,4594
Non-polymers2,2374
Water2,450136
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9242
Polymers18,3651
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9242
Polymers18,3651
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9242
Polymers18,3651
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9242
Polymers18,3651
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 87.200, 105.000
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 protein 3 / nsP3 / Non-structural protein 3' / nsP3'


Mass: 18364.871 Da / Num. of mol.: 4 / Fragment: sequence database residues 1330-1489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Strain: P676 / Gene: nsP3 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P36328
#2: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.2M AmSO4, 0.1 M Na Cacodylate, 30 % PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 20549 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.72 / Rsym value: 0.497 / % possible all: 89.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GQE

3gqe


Resolution: 2.6→29.74 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0 / SU B: 24.265 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 36.706 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1072 5 %RANDOM
Rwork0.195 ---
obs0.199 20334 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-0 Å2
2--2.41 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 144 136 5136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9896787
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18624.948192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.09515780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2551520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213666
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3971.53171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76625065
X-RAY DIFFRACTIONr_scbond_it1.28731809
X-RAY DIFFRACTIONr_scangle_it2.2034.51721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 78 -
Rwork0.234 1476 -
obs--100 %
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)
11.6326-0.0554-0.6061.4669-0.0422.46470.00710.0043-0.0070.0337-0.06750.1015-0.0113-0.17460.06040.05510.0091-0.00950.0506-0.01840.06-17.3973-19.700527.0475
26.6954-1.06030.29156.6215-4.31948.5621-0.1405-0.12970.4092-0.50280.14880.1396-0.51670.483-0.00830.2781-0.0791-0.00690.0871-0.0390.1599-12.2377-3.54923.5544
31.9487-0.26170.0051.38880.06651.34530.0507-0.00880.13760.05450.0762-0.1815-0.07230.1158-0.12690.07280.0014-0.0070.1083-0.03590.0618-40.8159-1.0432.7275
48.2193-0.2548-0.98031.627-0.35310.945-0.09690.1269-0.1727-0.00210.0446-0.12680.07520.09970.05240.22570.015-0.01110.2217-0.01320.1628-33.2809-11.803113.9278
51.44780.1708-0.30382.4262-0.0921.4141-0.0166-0.0318-0.0866-0.05290.0206-0.14880.06340.1733-0.00410.0701-0.00330.01390.0952-0.03560.0524-38.0373-5.177750.9483
62.6277-3.39392.94947.4858-0.04018.17860.11090.0444-0.1761-0.7507-0.23980.5049-0.3488-0.24150.12890.3515-0.0466-0.06070.267-0.05090.0789-44.5458-3.864635.8113
72.02150.033-0.3431.75710.70321.8591-0.05690.17360.0093-0.075-0.04350.15830.0598-0.17740.10040.0441-0.0230.00330.1119-0.02460.0639-14.736919.122731.8523
88.2394-0.2356-0.59531.9741-1.14462.4701-0.0352-0.1842-0.00330.0550.01870.21210.222-0.18630.01660.2791-0.04320.04920.1933-0.01190.2267-22.52087.672642.216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 143
2X-RAY DIFFRACTION2A144 - 160
3X-RAY DIFFRACTION3B-1 - 141
4X-RAY DIFFRACTION4B142 - 158
5X-RAY DIFFRACTION5C0 - 141
6X-RAY DIFFRACTION6C142 - 159
7X-RAY DIFFRACTION7D0 - 143
8X-RAY DIFFRACTION8D144 - 160

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