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

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Basic information

Entry
Database: PDB / ID: 3gqe
TitleCrystal structure of macro domain of Venezuelan Equine Encephalitis virus
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / macro domain / X domain / Venezuelan Equine Encephalitis virus / alphavirus / virus / VIZIER. Viral enzymes involved in replication / ATP-binding / Cell membrane / Cell projection / Endosome / Helicase / Hydrolase / Lipoprotein / Lysosome / Membrane / Methyltransferase / mRNA capping / mRNA processing / Multifunctional enzyme / Nucleotide-binding / Nucleotidyltransferase / Nucleus / Palmitate / Phosphoprotein / Protease / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 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 / nucleoside-triphosphate phosphatase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase ...: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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. / 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
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsJamal, S. / Malet, H. / Coutard, B. / 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 / Derived calculations / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8933
Polymers36,7302
Non-polymers1631
Water2,846158
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5282
Polymers18,3651
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,3651
Polymers18,3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.610, 129.610, 42.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Non-structural protein 3 / nsP3 / Non-structural protein 3' / nsP3'


Mass: 18364.871 Da / Num. of mol.: 2 / 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-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 11mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9749 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 2.3→34.269 Å / Num. all: 15980 / Num. obs: 15851 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2317 / Rsym value: 0.264 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GPG

3gpg


Resolution: 2.3→34.26 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.307 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.832 / SU B: 15.88 / SU ML: 0.181 / SU R Cruickshank DPI: 0.359 / SU Rfree: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 812 5.1 %RANDOM
Rwork0.203 ---
obs0.206 15850 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.18 Å2 / Biso mean: 17.872 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 11 158 2594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222465
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9563346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02825.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64715402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.146158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211866
X-RAY DIFFRACTIONr_mcbond_it0.5491.51609
X-RAY DIFFRACTIONr_mcangle_it1.00722575
X-RAY DIFFRACTIONr_scbond_it1.7733856
X-RAY DIFFRACTIONr_scangle_it2.944.5771
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 45 -
Rwork0.231 1140 -
all-1185 -
obs--99.92 %
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)
14.01172.4337-0.28726.4024-0.30253.2964-0.03680.008-0.1724-0.419-0.2878-0.20360.43140.14970.32460.16260.04440.09310.11420.01910.063959.506813.18384.5793
27.79531.5166-1.22.56680.46320.83340.0790.06770.5764-0.00570.0246-0.5127-0.24570.0615-0.10360.2224-0.0508-0.00650.1516-0.00860.341166.059329.68077.9733
32.5802-0.145-0.73982.10980.76763.3084-0.0210.00880.1581-0.1772-0.0380.0623-0.057-0.05080.0590.0531-0.0080.03820.0758-0.02310.070154.426521.58838.8367
49.64763.00292.97218.08083.42785.9354-0.10440.0574-0.0124-0.0429-0.052-0.1444-0.04260.11970.15640.16810.01240.0630.12270.08510.082155.65967.08616.4748
51.3838-1.1133-0.46181.96390.5594.45340.0775-0.1197-0.424-0.17290.12380.03580.2007-0.1162-0.20140.0913-0.0015-0.02630.14190.09040.267629.373811.6448.8766
67.0338-3.2136-2.31545.85942.95983.53880.2690.4267-0.8884-0.4955-0.22330.60850.3689-0.5506-0.04570.2437-0.0867-0.1850.18070.03740.294922.90327.70850.571
73.2557-1.4190.70382.937-0.74972.5944-0.1428-0.2875-0.327-0.03810.22240.20650.0867-0.238-0.07950.02220.00340.00430.18470.14470.133322.689217.478612.6563
81.6526-0.3188-3.21259.1104-0.34996.37230.01530.0835-0.10620.7619-0.13220.4042-0.1085-0.23910.11690.28410.0106-0.01440.44540.08550.16327.810420.86527.3318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 22
2X-RAY DIFFRACTION2A23 - 54
3X-RAY DIFFRACTION3A55 - 143
4X-RAY DIFFRACTION4A144 - 160
5X-RAY DIFFRACTION5B1 - 38
6X-RAY DIFFRACTION6B39 - 59
7X-RAY DIFFRACTION7B60 - 151
8X-RAY DIFFRACTION8B152 - 159

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