[English] 日本語
Yorodumi
- PDB-5aoo: X-ray structure of a human Kobuvirus: Aichi virus A (AiV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aoo
TitleX-ray structure of a human Kobuvirus: Aichi virus A (AiV)
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / AICHI VIRUS / KOBUVIRUS / PICORNAVIRUS / ACUTE GASTROENTERISIS / ICOSAHEDRAL CAPSID / FULL VIRUS PARTICLE
Function / homology
Function and homology information


host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase ...host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / 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 / ATP binding / membrane
Similarity search - Function
LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus ...LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesAICHIVIRUS A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSabin, C. / Palkova, L. / Plevka, P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: The Use of Noncrystallographic Symmetry Averaging to Solve Structures from Data Affected by Perfect Hemihedral Twinning
Authors: Sabin, C. / Plevka, P.
History
DepositionSep 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Refinement description
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: VP0
B: VP1
C: VP3


Theoretical massNumber of molelcules
Total (without water)90,2283
Polymers90,2283
Non-polymers00
Water2,648147
1
A: VP0
B: VP1
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,413,661180
Polymers5,413,661180
Non-polymers00
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP0
B: VP1
C: VP3
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)451,13815
Polymers451,13815
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP0
B: VP1
C: VP3
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)541,36618
Polymers541,36618
Non-polymers00
Water32418
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)350.816, 350.816, 350.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(0.5, 0.809, -0.309), (-0.809, 0.309, -0.5), (-0.309, 0.5, 0.809)
2generate(0.5, -0.809, -0.309), (0.809, 0.309, 0.5), (-0.309, -0.5, 0.809)
3generate(-0.309, 0.5, -0.809), (-0.5, -0.809, -0.309), (-0.809, 0.309, 0.5)
4generate(-0.309, -0.5, -0.809), (0.5, -0.809, 0.309), (-0.809, -0.309, 0.5)

-
Components

#1: Protein VP0


Mass: 27194.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AICHIVIRUS A / References: UniProt: Q91QP4, UniProt: O91464*PLUS
#2: Protein VP1


Mass: 38950.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AICHIVIRUS A / References: UniProt: Q91QP4, UniProt: O91464*PLUS
#3: Protein VP3


Mass: 24082.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AICHIVIRUS A / References: UniProt: Q91QP4, UniProt: O91464*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 4.33 Å3/Da / Density % sol: 71.78 %
Description: FOR TWINNING ANALYSES AND CALCULATION OF INITIAL ROTATION FUNCTIONS THE AIV DIFFRACTION IMAGES WERE PROCESSED IN SPACEGROUP I23 TO 2.3 ANGSTROM RESOLUTION IN PROGRAM XDS. HOWEVER, SINCE ...Description: FOR TWINNING ANALYSES AND CALCULATION OF INITIAL ROTATION FUNCTIONS THE AIV DIFFRACTION IMAGES WERE PROCESSED IN SPACEGROUP I23 TO 2.3 ANGSTROM RESOLUTION IN PROGRAM XDS. HOWEVER, SINCE THE DATA ANALYSIS REVEALED THAT THE CRYSTAL WAS PERFECTLY HEMIHEDRALLY TWINNED THE IMAGES WERE RE-PROCESSED IN SPACE GROUP I432. TAKING ADVANTAGE OF THE HIGHER SYMMETRY ALLOWED US TO OBTAIN DATASET THAT WAS MORE THAN 90 PERCENT COMPLETE FROM FIRST 160 DIFFRACTION IMAGES, CORRESPONDING TO 16 DEG ROTATION RANGE, AND THE DATA COULD BE PROCESSED TO 2.1 ANGSTROM RESOLUTION. SUBSEQUENTLY, THE DATA WERE EXPANDED FROM I432 TO I23 USING THE PROGRAM SFTOOLS FROM CCP4 PACKAGE.
Crystal growpH: 7.5
Details: 0.05M CADMIUM SULFATE 0.1M HEPES PH 7.5 1.0M SODIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→71.46 Å / Num. obs: 186646 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.1 / % possible all: 83.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
GLRFphasing
MOLREPphasing
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEV

1bev


Resolution: 2.1→71.46 Å / Stereochemistry target values: ENGH & HUBER /
RfactorNum. reflection
Rwork0.3301 -
obs0.3301 367359
Displacement parametersBiso mean: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 0 147 5938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.93
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.571
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5CNS_TOPPAR:CARBOHYDRATE.PARAM

+
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