[English] 日本語
Yorodumi
- PDB-7vw5: Crystal structures of alphavirus nonstructural protein 4 (nsP4) r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vw5
TitleCrystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold
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


O-acetyl-ADP-ribose deacetylase activity / positive stranded viral RNA replication / 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 ...O-acetyl-ADP-ribose deacetylase activity / positive stranded viral RNA replication / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / 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
Similarity search - Domain/homology
Biological speciesSindbis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,8024
Polymers116,7542
Non-polymers492
Water6,233346
1
A: RNA-directed RNA polymerase nsP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4012
Polymers58,3771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area22870 Å2
MethodPISA
2
B: RNA-directed RNA polymerase nsP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4012
Polymers58,3771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.450, 68.940, 71.420
Angle α, β, γ (deg.)116.311, 107.050, 95.104
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

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


Mass: 58376.809 Da / Num. of mol.: 2 / Mutation: C164S
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 II / References: UniProt: P03317, RNA-directed RNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 18-20% PEG3350, 0.2 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 1.91→45.69 Å / Num. obs: 144300 / % possible obs: 87.5 % / Redundancy: 1.826 % / Biso Wilson estimate: 40.913 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.105 / Χ2: 0.975 / Net I/σ(I): 6.21 / Num. measured all: 263495
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
1.91-2.031.7411.6580.563690726612211990.5612.34479.7
2.03-2.171.8050.8081.124112925022227810.4321.14391
2.17-2.341.8990.252.023308523218174250.9920.35475
2.34-2.571.8730.2253.233854121470205760.8980.31895.8
2.57-2.871.7780.1295.163249219404182730.9650.18394.2
2.87-3.311.8320.0699.072997117118163620.990.09795.6
3.31-4.051.8940.04815.392215914448117020.9940.06781
4.05-5.71.7920.03519.731857511258103660.9950.04992.1
5.7-45.691.8940.02623.0210636627856160.9980.03789.5

-
Processing

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

7f0s


Resolution: 2.3→36.27 Å / SU ML: 0.2774 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.2681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Refined to 2.3 Angstrom resolution to have best values of mean I/sigma (larger than 2), data completeness (94%) and other parameters (R-factors/clashscore/etc.).
RfactorNum. reflection% reflection
Rfree0.2405 1169 2.62 %
Rwork0.1967 43507 -
obs0.1978 44676 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7267 0 2 346 7615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00177405
X-RAY DIFFRACTIONf_angle_d0.43710061
X-RAY DIFFRACTIONf_chiral_restr0.0381176
X-RAY DIFFRACTIONf_plane_restr0.0031302
X-RAY DIFFRACTIONf_dihedral_angle_d4.23531006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.33951390.25685365X-RAY DIFFRACTION93.7
2.4-2.530.25231480.22935498X-RAY DIFFRACTION95.42
2.53-2.690.2691450.22385350X-RAY DIFFRACTION93.06
2.69-2.90.26631500.215537X-RAY DIFFRACTION96.15
2.9-3.190.23331540.21075633X-RAY DIFFRACTION97.18
3.19-3.650.27041430.19945374X-RAY DIFFRACTION93.37
3.65-4.60.2231400.16655190X-RAY DIFFRACTION89.79
4.6-36.270.19231500.17445560X-RAY DIFFRACTION96.8
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)
10.3649494090630.08945977828420.01417539694890.35049175113-0.2459260488030.2731988068910.009129204119-0.150398027217-0.04951258038310.0432467062435-0.01236249343950.1010109139480.009974248818670.007994343992-0.01358168874440.1830421071890.0122762199747-8.42612476671E-50.182030693308-0.009400247585540.159635111043-3.6579780479628.4452505422-6.3146869247
20.547673200604-0.2477423177840.1861281162420.367968196063-0.2357306862010.7393190269440.0370728740143-0.011007145963-0.0329459859008-0.06841261267250.00773275299188-0.09968439575080.2478338032030.1226469577840.02729409757950.190729472650.00282686238533-0.01017686414290.2011575836060.008249824254390.15043233833313.212302092627.4355057568.20452214969
30.986631571251-0.525949092537-0.0947195402530.521080312484-0.04406795369050.0301141007368-0.0870212060035-0.06158768807090.08962233191940.08781580497480.0808539482985-0.02418882143980.08129849333930.0116006251134-0.003418869691440.1346228412390.0146617395758-0.01211934054330.131978340957-0.008734626912340.0846648691554-4.3310265061645.6986203548.78668289435
40.589357332872-0.09546540805210.03675966477360.3885898562420.2168157665220.3013773230850.0146514951702-0.0417121973383-0.104881805629-0.0727917551433-0.0140026105688-0.0516888324198-0.0755077556254-0.03667576160080.0414900819450.2077570963940.027837364390.02548141369880.1675768766680.01688793392870.125915367148-19.99474154350.4455275225-6.76720672652
50.58844657321-0.2066164207880.3528160352380.4507551955050.1154995885710.6946445778610.0396219112922-0.0123633939001-0.09023839089520.004493488747570.04349410962090.0230087614473-0.116255218138-0.2218558730160.1246553622440.1368951528760.00758998042445-0.008730172837960.2150417924970.06535882794690.195371596296-27.89064685457.2808649744-25.7275863549
60.369662056125-0.04740036077190.07388313973570.3341566849570.06222568666290.5727795357830.008743300880480.0629002868294-0.02962191575820.01144862261370.0181279612245-0.07076589016820.0440836593775-0.05512992225090.01035863370440.1668575453960.0205241260010.01017522324430.0977933237083-0.003206990466780.124611824239-8.0932045012451.229083825-23.2593738625
70.606391554754-0.2436563947920.06724896268970.6650723822820.05098125925940.5096877356470.075841190054-0.0124909325321-0.0461235828827-0.0970242413007-0.03404333864870.163663711784-0.0951585784684-0.04795820164650.2209199684220.1035454156250.0048844359937-0.01735435802340.0995027143468-0.03765144070840.129656197989-6.0114967490925.1929149264-23.8159667296
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 192 )AA104 - 1921 - 75
22chain 'A' and (resid 193 through 336 )AA193 - 33676 - 199
33chain 'A' and (resid 337 through 601 )AA337 - 601200 - 464
44chain 'B' and (resid 104 through 213 )BB104 - 2131 - 96
55chain 'B' and (resid 214 through 336 )BB214 - 33697 - 200
66chain 'B' and (resid 337 through 506 )BB337 - 506201 - 370
77chain 'B' and (resid 507 through 602 )BB507 - 602371 - 466

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more