[English] 日本語
Yorodumi
- PDB-4z92: crystal structure of parechovirus-1 virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z92
Titlecrystal structure of parechovirus-1 virion
Components
  • Capsid subunit VP3
  • RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
  • capsid subunit VP0
  • capsid subunit VP1
KeywordsVIRUS / parechovirus / picornavirus / virion / pathogen
Function / homology
Function and homology information


host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
RNA / Genome polyprotein
Similarity search - Component
Biological speciesHuman parechovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKalynych, S. / Palkova, L. / Plevka, P.
CitationJournal: J.Virol. / Year: 2015
Title: The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid.
Authors: Kalynych, S. / Palkova, L. / Plevka, P.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: cell / chem_comp_atom ...cell / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_oper
Item: _cell.Z_PDB / _database_2.pdbx_DOI ..._cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: capsid subunit VP1
B: Capsid subunit VP3
C: capsid subunit VP0
D: RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,2194
Polymers88,2194
Non-polymers00
Water00
1
A: capsid subunit VP1
B: Capsid subunit VP3
C: capsid subunit VP0
D: RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)5,293,150240
Polymers5,293,150240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area11610 Å2
ΔGint-61 kcal/mol
Surface area34830 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: capsid subunit VP1
B: Capsid subunit VP3
C: capsid subunit VP0
D: RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
x 5


  • icosahedral pentamer
  • 441 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)441,09620
Polymers441,09620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid subunit VP1
B: Capsid subunit VP3
C: capsid subunit VP0
D: RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
x 6


  • icosahedral 23 hexamer
  • 529 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)529,31524
Polymers529,31524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)399.500, 399.500, 332.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.642324, -0.755791, 0.127343), (-0.178391, -0.309024, -0.934235), (0.745348, 0.57738, -0.3333)148.0114, 264.3406, -104.5197
3generate(-0.142303, -0.467073, 0.872691), (0.467127, -0.808997, -0.356855), (0.872656, 0.356885, 0.3333)209.4198, 145.0114, -159.9919
4generate(0.475675, 0.46709, -0.745391), (0.11029, 0.809025, 0.577345), (0.872691, -0.356855, 0.3333)112.894, -48.0498, -77.6859
5generate(0.745367, 1.0E-5, 0.666693), (1.0E-5, -1.000067, -5.4E-5), (0.666693, -5.4E-5, -0.7453)-4.6171, 230.6623, 12.0694
6generate(0.475653, -0.467073, -0.745348), (-0.110273, 0.809047, -0.57738), (0.872657, 0.356885, 0.3333)220.628, 92.0956, -159.9919
7generate(0.642344, 0.755773, 0.127352), (0.178373, -0.309044, 0.93418), (0.745391, -0.577345, -0.3333)-26.3162, 37.599, 28.6416
8generate(0.563654, 0.755753, 0.33335), (-0.755747, 0.309046, 0.577379), (0.333306, -0.577296, 0.7454)-27.7376, 182.5989, 21.1858
9generate(-0.142303, 0.467127, 0.872657), (-0.467073, -0.808997, 0.356885), (0.872691, -0.356855, 0.3333)101.6851, 272.224, -77.6859
10generate(0.563654, -0.755748, 0.333306), (0.755753, 0.309046, -0.577296), (0.33335, 0.577379, 0.7454)46.5813, -23.2369, -111.987

-
Components

#1: Protein capsid subunit VP1


Mass: 26417.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Cell line (production host): A549 / Organ (production host): Lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma / References: UniProt: Q66578
#2: Protein Capsid subunit VP3


Mass: 28293.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Cell line: A549 / Cell line (production host): A549 / Organ (production host): lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma / References: UniProt: Q66578
#3: Protein capsid subunit VP0


Mass: 31693.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Cell line (production host): A549 / Organ (production host): Lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma / References: UniProt: Q66578
#4: RNA chain RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')


Mass: 1815.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Cell line (production host): A549 / Organ (production host): Lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.0, 0.6M ammonium sulfate, 0.1M MgCl2, 5% (w/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.09→65 Å / Num. obs: 233083 / % possible obs: 78.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.354 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 0.9 / % possible all: 31.8

-
Processing

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEV

1bev


Resolution: 3.1→65 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rwork0.29 --
obs-233083 78.2 %
Refinement stepCycle: LAST / Resolution: 3.1→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 119 0 0 5404

+
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