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- PDB-7vb4: A crystal structure of alphavirus nonstructural protein 4 (nsP4) ... -

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Basic information

Entry
Database: PDB / ID: 7vb4
TitleA crystal structure of alphavirus nonstructural protein 4 (nsP4) reveals an intrinsically dynamic RNA-dependent RNA polymerase
ComponentsRNA-directed RNA polymerase nsP4
KeywordsTRANSFERASE / RNA dependent RNA polymerase / RNA directed RNA polymerase / RdRp / Alphavirus / NSP4 / nonstructural protein 4
Function / homology
Function and homology information


positive stranded viral RNA replication / 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 ...positive stranded viral RNA replication / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / symbiont-mediated suppression of host innate immune response / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase / 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 / (+) 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
Similarity search - Domain/homology
Biological speciesSindbis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTan, Y.B. / Luo, D.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2016T22097 Singapore
National Research Foundation (NRF, Singapore)OFIRG17nov084 Singapore
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold.
Authors: Tan, Y.B. / Lello, L.S. / Liu, X. / Law, Y.S. / Kang, C. / Lescar, J. / Zheng, J. / Merits, A. / Luo, D.
History
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase nsP4
B: RNA-directed RNA polymerase nsP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,25110
Polymers116,7862
Non-polymers4668
Water15,781876
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-90 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 68.290, 71.070
Angle α, β, γ (deg.)115.969, 106.713, 95.900
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein RNA-directed RNA polymerase nsP4 / Non-structural protein 4 / nsP4


Mass: 58392.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Plasmid: pSUMO-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta T1R / References: UniProt: P03317, RNA-directed RNA polymerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Magnesium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→45.001 Å / Num. obs: 156684 / % possible obs: 88.4 % / Redundancy: 3.455 % / Biso Wilson estimate: 38.036 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.074 / Χ2: 0.95 / Net I/σ(I): 13.2 / Num. measured all: 541271
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.86-1.972.9440.9121.275407328744183660.5421.12863.9
1.97-2.113.3570.4712.727665526762228360.8530.56385.3
2.11-2.273.6780.2795.158415025000228790.9540.32791.5
2.27-2.493.5210.1747.877714323020219080.9770.20595.2
2.49-2.783.5740.1111.877151520838200080.990.1396
2.78-3.213.6430.06418.576442518444176830.9960.07595.9
3.21-3.933.3940.03528.545067915558149330.9980.04296
3.93-5.533.5130.02938.034069212064115830.9980.03496
5.53-45.0013.3810.02940.1621939672864880.9980.03496.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F0S

7f0s


Resolution: 1.86→45 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 24.0026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 1927 2.44 %
Rwork0.1872 76935 -
obs0.1881 78862 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.91 Å2
Refinement stepCycle: LAST / Resolution: 1.86→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 28 876 8064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337318
X-RAY DIFFRACTIONf_angle_d0.62399933
X-RAY DIFFRACTIONf_chiral_restr0.04251156
X-RAY DIFFRACTIONf_plane_restr0.00491281
X-RAY DIFFRACTIONf_dihedral_angle_d5.7585999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.3701760.33312999X-RAY DIFFRACTION48.9
1.9-1.960.35371110.30724353X-RAY DIFFRACTION70.62
1.96-2.010.30921260.27695121X-RAY DIFFRACTION82.97
2.01-2.080.2751370.23335373X-RAY DIFFRACTION88.01
2.08-2.150.24411440.20315733X-RAY DIFFRACTION92.86
2.15-2.240.2311430.18415744X-RAY DIFFRACTION93.56
2.24-2.340.22881450.18515794X-RAY DIFFRACTION94.42
2.34-2.460.23711430.18475852X-RAY DIFFRACTION94.86
2.46-2.620.24871490.18655910X-RAY DIFFRACTION95.95
2.62-2.820.22491470.185901X-RAY DIFFRACTION96.21
2.82-3.10.2071490.17895965X-RAY DIFFRACTION97.23
3.1-3.550.20931520.16446042X-RAY DIFFRACTION98.07
3.55-4.470.18361520.15266054X-RAY DIFFRACTION98.65
4.48-450.20721530.17916094X-RAY DIFFRACTION99.1
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)
10.267764077557-0.0206162494083-0.05016232070820.0710005918361-0.02082111121110.0625735535466-0.0261555960197-0.19085518822-0.0612393795752-0.04405395911930.03146071794560.1074339245980.1309450783820.1039342766930.005880649053890.1117282705580.0261074008669-0.007923987784830.104447550334-0.01540968273370.0998294401393-0.19961990063729.3951971538-6.64084172905
20.117694997643-0.0361116007226-0.0179790855560.04527632138250.04079379356240.240947202971-0.16646068191-0.10426340756-0.0500764856710.1171587664740.0603092185597-0.06848105951730.2619064751840.13833963827-0.141734850491-0.02611800308680.0717373194126-0.1109889598420.2336268211780.0988522659255-0.0033803270026312.561451390326.62451658411.6691708027
30.331612063653-0.302098953986-0.0997234030520.112621348143-0.1226700972220.236391082226-0.186444855877-0.1211834982890.05208869938040.165268758070.1327102859080.04349468177760.1293505353910.113707743346-0.03478481330070.0149109539542-0.0154233231565-0.04390102206120.0717213563853-0.06015804653140.0525117345168-1.7621757251445.80713250598.1532091669
40.0443438753610.02468653002160.0265050431070.03988125832190.008363082200710.0159579855211-0.0706323648831-0.0891297773894-0.1271125742130.05143532797430.03565598915630.07538623209710.0796908906534-0.101714075504-0.00716506224151-0.0599950188824-0.1080181807010.2180637079260.04128397519410.0949196029342-0.0698307495464-28.928877706742.249401188810.3288875136
50.121128368936-0.007615953111840.001809022707870.1207106170140.03238925409830.05970938574010.0242622935235-0.00689859720912-0.0470449863816-0.114846678078-0.02761817445750.0595959331777-0.0416724954402-0.1294246163510.01250636597980.119783015473-0.002608186019230.01068218073190.09662010718340.002578150811560.0861737184724-20.007792282448.5984034075-7.31232166197
60.15190047526-0.05844942828040.1089026245260.21318769262-0.08035619642890.2467976602150.002776361150410.05874336795930.0578021548030.02694366013530.02840202316750.0233182124384-0.0229546562134-0.0684940416122-0.00414036329640.0878199675326-0.003162784945650.005426666336890.08110591434150.02208259176840.0710743769787-20.407841852254.8165665674-26.9151108649
70.178684696634-0.2387896908270.08172174109970.210505005941-0.02671478654440.23189424610.06785980536160.062712176126-0.0324593712904-0.068861611401-0.05042163226150.00868637705806-0.00198337543577-0.01551688850430.0007764119383370.0723977617393-0.00821209892110.02403653397820.0286010406995-0.01633717453790.0692282205492-6.8808310359639.0266137272-22.8012944454
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 104 through 213 )AA104 - 2131 - 91
22chain 'A' and (resid 214 through 336 )AA214 - 33692 - 190
33chain 'A' and (resid 337 through 577 )AA337 - 577191 - 431
44chain 'A' and (resid 578 through 602 )AA578 - 602432 - 456
55chain 'B' and (resid 104 through 213 )BB104 - 2131 - 93
66chain 'B' and (resid 214 through 396 )BB214 - 39694 - 256
77chain 'B' and (resid 397 through 601 )BB397 - 601257 - 461

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