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- PDB-7f0s: A crystal structure of alphavirus nonstructural protein 4 (nsP4) ... -

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Basic information

Entry
Database: PDB / ID: 7f0s
TitleA crystal structure of alphavirus nonstructural protein 4 (nsP4) reveals an intrinsically 1dynamic 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


: / ADP-ribose 1''-phosphate phosphatase / polynucleotide adenylyltransferase / host cell cytoplasmic vesicle membrane / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription ...: / ADP-ribose 1''-phosphate phosphatase / polynucleotide adenylyltransferase / host cell cytoplasmic vesicle membrane / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / membrane / metal ion binding
Similarity search - Function
Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / 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. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesRoss river virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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
DepositionJun 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase nsP4


Theoretical massNumber of molelcules
Total (without water)54,2251
Polymers54,2251
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20290 Å2
Unit cell
Length a, b, c (Å)64.837, 68.349, 99.646
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 RNA-directed RNA polymerase nsP4 / Non-structural protein 4 / nsP4


Mass: 54224.840 Da / Num. of mol.: 1 / Mutation: Q192A,Q196A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ross river virus (strain T48) / Strain: T48 / Plasmid: pSUMO-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II T1R / References: UniProt: P13888, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThese UNK residues should be in between the missing residues of positions 135-184 but the author is ...These UNK residues should be in between the missing residues of positions 135-184 but the author is unsure the exact part/position corresponds with these residues. So the residue numbers of 141-145, 171-174 is meaningless. The correct sequence of 135-184 is as follows. TVASYQITDEYDAYLDMVDGSESCLDRATFCPAKLRCYPKHHAYHQPQVR

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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: 2.04 Å3/Da / Density % sol: 39.58 % / Description: hexagon
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES/TRIS, 24% PEG 3350, 0.2M Ammonium Acetate, 0.3% TMAO
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37774 / % possible obs: 99.8 % / Redundancy: 5.69 % / Biso Wilson estimate: 83.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.04
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.69 % / Rmerge(I) obs: 4.8 / Mean I/σ(I) obs: 0.36 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
CRANK2phasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→27.13 Å / SU ML: 0.525 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.16
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 1305 4.98 %RANDOM
Rwork0.2653 ---
obs0.2664 26213 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 0 1 3099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063159
X-RAY DIFFRACTIONf_angle_d0.9764297
X-RAY DIFFRACTIONf_dihedral_angle_d13.715435
X-RAY DIFFRACTIONf_chiral_restr0.05522
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.4641420.38422787X-RAY DIFFRACTION100
2.7-2.830.41061360.34732790X-RAY DIFFRACTION100
2.83-2.980.35711430.33572777X-RAY DIFFRACTION100
2.98-3.160.33561560.33772733X-RAY DIFFRACTION100
3.16-3.410.35251420.30822801X-RAY DIFFRACTION100
3.41-3.750.30161510.28162754X-RAY DIFFRACTION100
3.75-4.290.30181420.24932784X-RAY DIFFRACTION100
4.29-5.40.25051470.23792768X-RAY DIFFRACTION100
5.4-27.130.25181460.24162714X-RAY DIFFRACTION98
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)
10.782-0.3149-0.52840.13580.32950.4906-1.6519-1.5385-0.4883-0.70440.71831.14812.09540.9166-0.00871.3431-0.26080.23781.32960.15751.906248.6967-14.712560.4819
21.21751.04470.00790.5552-0.19831.7109-0.09520.1267-0.2272-0.19220.0947-0.18430.05850.0976-0.00010.6694-0.04210.05350.5964-0.01090.583351.298-11.19444.047
32.868-0.8658-1.12872.61420.10453.0543-0.04010.3171-0.7029-0.2559-0.01080.34460.3443-0.40840.00010.6677-0.1452-0.09560.681-0.01170.743565.81854.820134.2302
4-0.63921.11731.14814.0941-1.0409-0.1488-0.1388-0.0133-0.24090.41640.1995-0.3763-0.0918-0.3250.79390.86520.05470.25180.71440.0780.95356.1999-1.858955.5317
50.0028-0.01130.06050.0382-0.04140.0406-0.264-0.7266-0.1038-0.06420.34910.2877-0.1052-0.11620.00021.1527-0.3869-0.2341.55020.42641.069965.9126-0.240848.0754
60.74220.00350.42220.09910.08910.40490.33390.1987-0.0122-0.35830.7010.23310.23290.72440.0480.98290.0786-0.19950.85460.28922.227676.93354.221746.059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 111 THROUGH 131 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 132 THROUGH 134 ) AND (RESID 185 THROUGH 349 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 350 THROUGH 490 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 491 THROUGH 600 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 141 THROUGH 145 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 171 THROUGH 174 )

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