[English] 日本語
Yorodumi
- PDB-4nz0: The EMCV 3Dpol structure at 2.8A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nz0
TitleThe EMCV 3Dpol structure at 2.8A resolution
ComponentsGenome polyprotein
KeywordsTRANSFERASE / Encephalomyocarditis virus / Close right hand / RNa dependent RNA polymerase
Function / homology
Function and homology information


positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMengo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVives-adrian, L. / Ferrer-orta, C. / Verdaguer, N.
CitationJournal: J.Virol. / Year: 2014
Title: The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site
Authors: Vives-Adrian, L. / Lujan, C. / Oliva, B. / van der Linden, L. / Selisko, B. / Coutard, B. / Canard, B. / van Kuppeveld, F.J. / Ferrer-Orta, C. / Verdaguer, N.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,23915
Polymers313,4676
Non-polymers7729
Water1,54986
1
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,2451
Polymers52,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5565
Polymers52,2451
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5214
Polymers52,2451
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4293
Polymers52,2451
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Genome polyprotein
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9858
Polymers104,4892
Non-polymers4966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)230.400, 140.786, 170.579
Angle α, β, γ (deg.)90.00, 125.86, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Genome polyprotein / Leader protein / Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Rho / Virion protein 4 / Protein VP2 / ...Leader protein / Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Rho / Virion protein 4 / Protein VP2 / Beta / P1B / Virion protein 2 / Protein VP3 / Gamma / P1C / Virion protein 3 / Protein VP1 / Alpha / P1D / Virion protein 1 / Protein 2A / P2A / G / Protein 2B / I / P2B / Protein 2C / C / P2C / Protein 3A / P3A / Protein 3B / P3B / H / VPg / Protease 3C / P3C / Picornain 3C / p22 / RNA-directed RNA polymerase 3D-POL / E / P3D-POL


Mass: 52244.504 Da / Num. of mol.: 6 / Fragment: UNP residues 1834-2293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLyS / References: UniProt: P12296, RNA-directed RNA polymerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHOR STATES THE CONFLICT IS DUE TO THE USED CONSTRUCT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 4.0M Ammonium acetate, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2013
RadiationMonochromator: CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→138.2 Å / Num. obs: 119540 / % possible obs: 98 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 16.3 / Rsym value: 0.49 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U09

1u09


Resolution: 2.8→138.2 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.917 / SU B: 49.959 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R: 0.92 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5370 5 %RANDOM
Rwork0.246 ---
obs0.247 101992 98.8 %-
all-275543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20.58 Å2
2---0.55 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→138.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22086 0 49 86 22221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01922690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221619
X-RAY DIFFRACTIONr_angle_refined_deg0.7681.97230744
X-RAY DIFFRACTIONr_angle_other_deg0.669349750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24652758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.33323.1951064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.688153858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.44115188
X-RAY DIFFRACTIONr_chiral_restr0.0460.23384
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02125447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5814.92411041
X-RAY DIFFRACTIONr_mcbond_other0.5814.92411040
X-RAY DIFFRACTIONr_mcangle_it1.0897.38413793
X-RAY DIFFRACTIONr_mcangle_other1.0897.38413794
X-RAY DIFFRACTIONr_scbond_it0.284.92111647
X-RAY DIFFRACTIONr_scbond_other0.284.92111647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5897.37316951
X-RAY DIFFRACTIONr_long_range_B_refined2.14138.66425176
X-RAY DIFFRACTIONr_long_range_B_other2.14138.66525177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 398 -
Rwork0.379 7545 -
obs--98.84 %
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)
10.5990.2942-0.09971.14310.19451.862-0.0205-0.12070.07070.05360.04470.01830.1160.1872-0.02420.80570.0651-0.37460.2426-0.01570.183761.26991.833942.1227
21.48450.0407-0.0821.18740.37751.4136-0.213-0.0296-0.03970.30390.3198-0.3156-0.1333-0.0868-0.10680.98330.1175-0.43580.1331-0.09310.250454.723849.765534.528
30.64680.11010.19481.25510.10921.7370.07240.1381-0.0443-0.1882-0.2488-0.0132-0.0313-0.15550.17640.97090.1249-0.42850.2166-0.04710.21410.219175.559526.6779
41.63710.2437-0.1380.89160.25661.7168-0.11550.2348-0.1143-0.12070.03860.19680.08660.13450.07690.8190.0089-0.45960.098-0.02010.30823.2971-16.710137.651
50.51970.22820.5171.0066-0.11151.08690.0857-0.11320.001-0.07160.06170.07070.2538-0.0391-0.14740.9615-0.0629-0.44450.14090.02280.222642.095723.867-12.4811
60.78640.31670.45511.11330.29520.8858-0.0261-0.04110.0386-0.1067-0.0089-0.0062-0.11320.03160.0350.86760.0576-0.39770.1048-0.02740.19311.843224.97855.0105
70.07260.05830.00340.04970.00110.0022-0.03990.0078-0.0501-0.02920.0372-0.0237-0.0144-0.02780.00270.86230.0936-0.25490.41090.03260.328336.440215.941827.2968
80.2980.0586-0.58970.0155-0.12071.5541-0.0463-0.08030.08520.0571-0.0574-0.0159-0.15370.05520.10371.0241-0.0831-0.43140.10120.0390.67418.61712.53827.396
900000000000000-00.7043-0.2004-0.5010.2888-0.09290.6815.5114-4.29262.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 460
2X-RAY DIFFRACTION2B1 - 460
3X-RAY DIFFRACTION3C1 - 460
4X-RAY DIFFRACTION4D1 - 460
5X-RAY DIFFRACTION5E1 - 460
6X-RAY DIFFRACTION6F1 - 460
7X-RAY DIFFRACTION7A501 - 529
8X-RAY DIFFRACTION7B501 - 506
9X-RAY DIFFRACTION7C501 - 504
10X-RAY DIFFRACTION7D601 - 607
11X-RAY DIFFRACTION7E601 - 625
12X-RAY DIFFRACTION7F601 - 614
13X-RAY DIFFRACTION8D501 - 503
14X-RAY DIFFRACTION8E501 - 503
15X-RAY DIFFRACTION8F501 - 502
16X-RAY DIFFRACTION9D504

+
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