[English] 日本語
Yorodumi
- PDB-2wzr: The Structure of Foot and Mouth Disease Virus Serotype SAT1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wzr
TitleThe Structure of Foot and Mouth Disease Virus Serotype SAT1
Components(POLYPROTEIN) x 4
KeywordsVIRUS / CAPSID / RNA REPLICATION / RNA-DIRECTED RNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / HOST CYTOPLASMIC VESICLE / CAPSID PROTEIN
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / : / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase ...L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / : / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 ...Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / 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 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / 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
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsAdams, P. / Lea, S. / Newman, J. / Blakemore, W. / King, A. / Stuart, D. / Fry, E.
Citation
Journal: To be Published
Title: The Structure of Foot-and-Mouth Disease Virus Serotype Sat1.
Authors: Adams, P. / Lea, S. / Newman, J. / Blakemore, W. / King, A. / Stuart, D. / Fry, E.
#1: Journal: To be Published
Title: Using Capsid Sequence Data to Predict Cross Reactivity and Select Vaccines for Foot-and-Mouth Disease
Authors: Reeve, R. / Blignaut, B. / Esterhuysen, J.J. / Opperman, P. / Matthews, L. / Fry, E. / De Beer, T.A.P. / Theron, J. / Rieder, E. / Vosloo, W. / O'Neill, H.G. / Haydon, D.T. / Maree, F.F.
History
DepositionDec 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)81,9084
Polymers81,9084
Non-polymers00
Water00
1
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,914,479240
Polymers4,914,479240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 5


  • icosahedral pentamer
  • 410 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)409,54020
Polymers409,54020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 6


  • icosahedral 23 hexamer
  • 491 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)491,44824
Polymers491,44824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 60


  • crystal asymmetric unit, crystal frame
  • 4.91 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,914,479240
Polymers4,914,479240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)305.140, 305.140, 723.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.494194, -0.642336, 0.585813), (0.86918, 0.378489, -0.318235), (-0.01731, 0.666446, 0.745352)-0.01126, 0.00603, 0.00493
3generate(-0.324218, -0.170142, 0.930556), (0.764026, -0.627138, 0.151532), (0.557805, 0.760098, 0.333323)-0.0178, -0.00304, 0.01281
4generate(-0.324218, 0.764026, 0.557805), (-0.170142, -0.627138, 0.760098), (0.930556, 0.151532, 0.333323)-0.01059, -0.01468, 0.01276
5generate(0.494194, 0.86918, -0.01731), (-0.642336, 0.378489, 0.666446), (0.585813, -0.318235, 0.745352)0.00041, -0.0128, 0.00484
6generate(-0.803371, -0.106812, 0.585822), (-0.106812, -0.941978, -0.318227), (0.585822, -0.318227, 0.745349)-0.01078, 0.0067, 0.00484
7generate(-0.5, 0.866025, 1.0E-5), (-0.866025, -0.5, 7.0E-6), (1.1E-5, -5.0E-6, 1)0.00051, 0.00065
8generate(0.505635, 0.648955, -0.568499), (-0.862574, 0.36704, -0.348207), (-0.017309, 0.666438, 0.74536)0.01136, 0.00739, 0.00493
9generate(0.82378, -0.458039, -0.334044), (-0.101228, 0.460922, -0.881649), (0.557798, 0.760099, 0.333332)0.00677, 0.01759, 0.01281
10generate(0.014771, -0.925129, 0.379365), (0.365859, -0.348096, -0.86312), (0.930553, 0.151543, 0.333325)-0.00691, 0.01717, 0.01276
11generate(-0.544286, 0.8389, -4.0E-6), (0.8389, 0.544286, -7.0E-6), (-4.0E-6, -7.0E-6, -1)0.00053, -0.00029, 0.03959
12generate(0.460172, 0.667126, -0.58582), (0.887661, -0.332854, 0.318223), (0.017302, -0.666447, -0.745352)0.01172, -0.00645, 0.03466
13generate(0.817407, -0.433503, -0.37937), (0.143858, -0.48408, 0.863117), (-0.557809, -0.760093, -0.333327)0.00767, -0.01688, 0.02678
14generate(0.033732, -0.941955, 0.334039), (-0.364599, 0.299598, 0.881651), (-0.930553, -0.15153, -0.33333)-0.00601, -0.01716, 0.02683
15generate(-0.80784, -0.155567, 0.568501), (0.06496, 0.935163, 0.348211), (-0.585811, 0.318229, -0.745356)-0.01042, -0.00691, 0.03475
16generate(0.347657, -0.732088, -0.585818), (-0.732088, -0.602308, 0.318234), (-0.585818, 0.318234, -0.745349)0.01202, -0.00569, 0.03475
17generate(-0.454365, -0.890815, -3.0E-6), (-0.890815, 0.454365, 5.0E-6), (-3.0E-6, 5.0E-6, -1)0.00081, 0.00049, 0.03959
18generate(-0.998823, -0.04531, 0.017313), (-0.04531, 0.744178, -0.666443), (0.017313, -0.666443, -0.745355)0.00055, 0.01326, 0.03466
19generate(-0.533294, 0.635969, -0.5578), (0.635969, -0.133381, -0.760101), (-0.5578, -0.760101, -0.333325)0.01161, 0.01497, 0.02678
20generate(0.298876, 0.211517, -0.930556), (0.211517, -0.965555, -0.151537), (-0.930556, -0.151537, -0.333321)0.01869, 0.00326, 0.02683

-
Components

#1: Protein POLYPROTEIN


Mass: 24161.252 Da / Num. of mol.: 1 / Fragment: RESIDUES 725-943 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#2: Protein POLYPROTEIN


Mass: 24623.590 Da / Num. of mol.: 1 / Fragment: RESIDUES 285-503 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#3: Protein POLYPROTEIN


Mass: 24339.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 504-724 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#4: Protein POLYPROTEIN


Mass: 8784.136 Da / Num. of mol.: 1 / Fragment: RESIDUES 200-284 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
Sequence detailsVP1 105 PRO IN STRUCTURE NOT GLN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDescription: NONE

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.875
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.875 Å / Relative weight: 1
ReflectionResolution: 3→17 Å / Num. obs: 300769 / % possible obs: 60 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.23

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3→17 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.23 --
obs0.23 300769 60.1 %
Refinement stepCycle: LAST / Resolution: 3→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 0 0 5210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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