[English] 日本語
Yorodumi
- PDB-4zpb: Coxsackievirus B3 Polymerase - F364W mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zpb
TitleCoxsackievirus B3 Polymerase - F364W mutant
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.797 Å
AuthorsPeersen, O.B. / McDonald, S.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Design of a Genetically Stable High Fidelity Coxsackievirus B3 Polymerase That Attenuates Virus Growth in Vivo.
Authors: McDonald, S. / Block, A. / Beaucourt, S. / Moratorio, G. / Vignuzzi, M. / Peersen, O.B.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)52,5161
Polymers52,5161
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 74.610, 289.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1111-

HOH

-
Components

#1: Protein RNA-directed RNA polymerase


Mass: 52516.086 Da / Num. of mol.: 1 / Fragment: unp residues 1724-2185 / Mutation: F364W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Plasmid: pET26/Ub / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5UEA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085 M Tris pH 7.5, 1.2 M Ammonium Sulfate , 25% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.797→52.757 Å / Num. obs: 144867 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 19.97 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.098 / Χ2: 0.993 / Net I/σ(I): 14.79 / Num. measured all: 1052868
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.910.7620.6642.3515229323530230610.72198
1.91-2.040.9090.3824.3614924122103221020.413100
2.04-2.20.970.237.814951120578205770.248100
2.2-2.410.9870.15311.8614574618911189110.165100
2.41-2.690.9930.11116.5213207517084170840.119100
2.69-3.110.9960.07823.5811632615136151360.084100
3.11-3.810.9980.05732.339434312710127100.061100
3.81-5.370.9980.05136.372143986598650.054100
5.370.9980.04836.6641190542954210.05199.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 1.797→52.757 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 3736 2.58 %
Rwork0.1878 --
obs0.1888 144867 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.797→52.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 0 654 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083787
X-RAY DIFFRACTIONf_angle_d0.8345129
X-RAY DIFFRACTIONf_dihedral_angle_d12.1882260
X-RAY DIFFRACTIONf_chiral_restr0.053558
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7973-1.820.33271320.31514885X-RAY DIFFRACTION91
1.82-1.8440.3131400.26415137X-RAY DIFFRACTION100
1.844-1.86930.26821400.25455281X-RAY DIFFRACTION100
1.8693-1.8960.30311390.24885235X-RAY DIFFRACTION100
1.896-1.92430.2661370.23775235X-RAY DIFFRACTION100
1.9243-1.95430.26371410.23085264X-RAY DIFFRACTION100
1.9543-1.98640.26821370.21565241X-RAY DIFFRACTION100
1.9864-2.02060.24861410.21395233X-RAY DIFFRACTION100
2.0206-2.05740.25241420.215206X-RAY DIFFRACTION100
2.0574-2.09690.21611370.20795228X-RAY DIFFRACTION100
2.0969-2.13980.29191380.20275311X-RAY DIFFRACTION100
2.1398-2.18630.19131420.19055248X-RAY DIFFRACTION100
2.1863-2.23710.22941370.18855188X-RAY DIFFRACTION100
2.2371-2.29310.26021420.19015260X-RAY DIFFRACTION100
2.2931-2.35510.20091380.18755241X-RAY DIFFRACTION100
2.3551-2.42440.20271450.18695253X-RAY DIFFRACTION100
2.4244-2.50260.20751380.18215256X-RAY DIFFRACTION100
2.5026-2.59210.28211310.19295239X-RAY DIFFRACTION100
2.5921-2.69590.2451400.18915224X-RAY DIFFRACTION100
2.6959-2.81850.20931400.19375234X-RAY DIFFRACTION100
2.8185-2.96710.24491380.19595257X-RAY DIFFRACTION100
2.9671-3.1530.22261420.18445234X-RAY DIFFRACTION100
3.153-3.39640.22011380.17635286X-RAY DIFFRACTION100
3.3964-3.73810.20341310.16715231X-RAY DIFFRACTION100
3.7381-4.27880.18911350.15285240X-RAY DIFFRACTION100
4.2788-5.390.17361420.15525240X-RAY DIFFRACTION100
5.39-52.780.24441330.18435244X-RAY DIFFRACTION100

+
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://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