[English] 日本語
Yorodumi
- PDB-2wff: Equine Rhinitis A Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wff
TitleEquine Rhinitis A Virus
Components(P1) x 4
KeywordsVIRUS / CAPSID / PICORNAVIRUS
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEQUINE RHINITIS A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsFry, E.E. / Tuthill, T.J. / Harlos, K. / Walter, T.S. / Knowles, N.J. / Gropelli, E. / Rowlands, D.J. / Stuart, D.I.
CitationJournal: Plos Pathog. / Year: 2009
Title: Equine Rhinitis a Virus and its Low Ph Empty Particle: Clues Towards an Aphthovirus Entry Mechanism?
Authors: Tuthill, T.J. / Harlos, K. / Walter, T.S. / Knowles, N.J. / Groppelli, E. / Rowlands, D.J. / Stuart, D.I. / Fry, E.E.
History
DepositionApr 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Other / Version format compliance
Revision 1.2Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: P1
2: P1
3: P1
4: P1


Theoretical massNumber of molelcules
Total (without water)85,0444
Polymers85,0444
Non-polymers00
Water00
1
1: P1
2: P1
3: P1
4: P1
x 60


Theoretical massNumber of molelcules
Total (without water)5,102,611240
Polymers5,102,611240
Non-polymers00
Water0
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
1: P1
2: P1
3: P1
4: P1
x 5


  • icosahedral pentamer
  • 425 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)425,21820
Polymers425,21820
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: P1
2: P1
3: P1
4: P1
x 6


  • icosahedral 23 hexamer
  • 510 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)510,26124
Polymers510,26124
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)314.000, 497.800, 556.500
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.457142, -0.85202, 0.255114), (0.524609, 0.489942, 0.696234), (-0.718197, -0.184443, 0.670951)-36.84622, -158.43204, 88.4435
3generate(-0.421221, -0.853988, -0.305414), (-0.003184, -0.33535, 0.942088), (-0.906953, 0.3978, 0.138537)103.86027, -193.80694, 203.46919
4generate(-0.421221, -0.003184, -0.906953), (-0.853988, -0.33535, 0.3978), (-0.305414, 0.942088, 0.138537)227.66788, -57.23779, 186.11547
5generate(0.457142, 0.524609, -0.718197), (-0.85202, 0.489942, -0.184443), (0.255114, 0.696234, 0.670951)163.4787, 62.54148, 60.3646
6generate(-0.999279, -0.030511, -0.022608), (-0.030511, 0.290653, 0.956342), (-0.022608, 0.956342, -0.291374)60.92453, -196.49223, 267.12418
7generate(-0.456582, 0.840627, -0.291342), (-0.54831, -0.007991, 0.836237), (0.700635, 0.541556, 0.464573)100.57859, -156.83445, 90.67185
8generate(0.441519, 0.85461, 0.273317), (-0.85543, 0.309018, 0.415628), (0.27074, -0.417311, 0.867497)-41.54758, -61.40548, 20.14476
9generate(0.453878, -0.007885, 0.891029), (-0.527442, 0.803585, 0.275783), (-0.718192, -0.595138, 0.360571)-169.04045, -42.08491, 153.00895
10generate(-0.436584, -0.55492, 0.708137), (-0.017614, 0.792235, 0.609962), (-0.899491, 0.253827, -0.355651)-105.7092, -125.57311, 305.65063
11generate(0.444829, 0.555003, -0.702921), (0.555003, -0.786806, -0.270014), (-0.702921, -0.270014, -0.658023)160.6392, 41.71198, 363.12234
12generate(0.999346, 0.022565, 0.028269), (0.034873, -0.808561, -0.587378), (0.009603, 0.58798, -0.808819)-5.85022, 122.0365, 373.60333
13generate(0.448378, -0.845621, 0.289625), (0.013616, -0.317522, -0.948153), (0.89374, 0.429074, -0.130856)-43.74712, 196.90375, 208.55992
14generate(-0.446656, -0.849751, -0.280039), (0.52061, 0.007712, -0.85376), (0.727643, -0.527128, 0.438944)99.32073, 162.84973, 96.07649
15generate(-0.448849, 0.015883, -0.893466), (0.855206, -0.282322, -0.434647), (-0.259148, -0.959188, 0.113137)225.63842, 66.93594, 191.60132
16generate(-0.44555, -0.524492, 0.725529), (-0.524492, -0.503847, -0.686328), (0.725529, -0.686328, -0.050603)-109.08097, 157.99934, 197.57899
17generate(-0.999906, -0.011172, 0.007959), (-0.011172, 0.326611, -0.945093), (0.007959, -0.945093, -0.326705)54.60061, 196.44907, 275.10682
18generate(-0.468676, 0.844999, -0.257528), (0.844999, 0.343854, -0.409563), (-0.257528, -0.409563, -0.875179)93.9172, 61.52776, 395.65163
19generate(0.413999, 0.86082, 0.295963), (0.86082, -0.475946, 0.180178), (0.295963, 0.180178, -0.938052)-45.4654, -60.30794, 392.62459
20generate(0.428291, 0.014428, 0.903526), (0.014428, -0.999854, 0.009127), (0.903526, 0.009127, -0.428437)-170.92516, -0.68522, 270.20896
21generate(0.473657, -0.840103, 0.264341), (-0.520337, -0.024782, 0.853601), (-0.710562, -0.54186, -0.448875)-39.2298, -161.2013, 320.27146
22generate(-0.414046, -0.863922, -0.286713), (-0.863922, 0.273755, 0.422725), (-0.286713, 0.422725, -0.859709)99.7962, -62.60708, 392.60098
23generate(-0.436584, -0.017614, -0.899491), (-0.55492, 0.792235, 0.253827), (0.708137, 0.609962, -0.355651)226.56734, -36.75912, 260.1564
24generate(0.43719, 0.529253, -0.727156), (-0.020361, 0.814135, 0.580318), (0.899138, -0.238904, 0.366708)165.89022, -119.37842, 105.97162
25generate(0.99975, 0.020927, -0.007868), (0.001012, 0.309191, 0.950999), (0.022334, -0.95077, 0.309093)1.61855, -196.28791, 143.12477
26generate(-0.453659, -0.00583, -0.891156), (0.50142, 0.825008, -0.260653), (0.736731, -0.565091, -0.371349)225.31307, 39.98446, 263.54684
27generate(0.429581, 0.548038, -0.717715), (0.849227, 0.025062, 0.527432), (0.30704, -0.836078, -0.454642)164.13531, -132.25176, 293.08619
28generate(0.999346, 0.034873, 0.009603), (0.022565, -0.808561, 0.58798), (0.028269, -0.587378, -0.808819)-1.99709, -120.8652, 374.02432
29generate(0.46824, -0.836148, 0.28567), (-0.836148, -0.523822, -0.162686), (0.28567, -0.162686, -0.944418)-43.49479, 58.4083, 394.50748
30generate(-0.429766, -0.861304, -0.27103), (-0.5402, 0.485779, -0.68717), (0.723523, -0.148912, -0.674047)96.99061, 157.81886, 326.22864
31generate(-0.441375, 0.852504, -0.280046), (-0.84523, -0.499774, -0.189242), (-0.301289, 0.153177, 0.941149)97.80377, 64.14021, 20.52877
32generate(0.446589, 0.84539, 0.293044), (-0.512663, 0.510197, -0.690562), (-0.733304, 0.158164, 0.661248)-45.76541, 157.72679, 90.60051
33generate(0.43719, -0.020361, 0.899138), (0.529253, 0.814135, -0.238904), (-0.727156, 0.580318, 0.366708)-170.23945, 34.7093, 151.04485
34generate(-0.456582, -0.54831, 0.700635), (0.840627, -0.007991, 0.541556), (-0.291342, 0.836237, 0.464573)-103.59946, -134.90627, 118.32976
35generate(-0.999565, -0.00885, -0.028142), (-0.00885, -0.820032, 0.572249), (-0.028142, 0.572249, 0.819597)62.06036, -116.71697, 37.66638
36generate(0.421377, -0.006571, 0.906862), (0.864147, -0.300452, -0.403706), (0.275121, 0.953774, -0.120925)-171.40427, 60.29572, 223.47844
37generate(-0.462123, -0.529505, 0.711384), (0.527358, -0.809014, -0.259596), (0.712976, 0.255189, 0.653103)-105.68334, 40.35114, 51.53781
38generate(-0.999952, 0.003102, -0.00925), (0.003102, -0.797809, -0.602903), (-0.00925, -0.602903, 0.797761)58.15196, 126.13411, 42.59993
39generate(-0.448849, 0.855206, -0.259148), (0.015883, -0.282322, -0.959188), (-0.893466, -0.434647, 0.113137)93.6868, 199.09547, 209.01664
40generate(0.429581, 0.849227, 0.30704), (0.548038, 0.025062, -0.836078), (-0.717715, 0.527432, -0.454642)-48.18675, 158.40511, 320.80571
41generate(0.473657, -0.520337, -0.710562), (-0.840103, -0.024782, -0.54186), (0.264341, 0.853601, -0.448875)162.27526, 136.59047, 291.73348
42generate(0.453878, -0.527442, -0.718192), (-0.007885, 0.803585, -0.595138), (0.891029, 0.275783, 0.360571)164.41623, 123.54732, 107.05566
43generate(0.446589, -0.512663, -0.733304), (0.84539, 0.510197, 0.158164), (0.293044, -0.690562, 0.661248)167.73679, -56.11183, 62.42193
44generate(0.461863, -0.496425, -0.735014), (0.540524, -0.499495, 0.677007), (-0.703219, -0.709977, 0.037632)167.64804, -154.10415, 219.51459
45generate(0.478592, -0.501168, -0.720958), (-0.501168, -0.83013, 0.244368), (-0.720958, 0.244368, -0.648462)164.27262, -35.00757, 361.23693
46generate(-0.441375, -0.84523, -0.301289), (0.852504, -0.499774, 0.153177), (-0.280046, -0.189242, 0.941149)103.56641, -54.46697, 20.20697
47generate(-0.428801, 0.017518, -0.903229), (0.017518, -0.999463, -0.0277), (-0.903229, -0.0277, 0.428264)227.09377, 6.84928, 143.7461
48generate(0.461863, 0.540524, -0.703219), (-0.496425, -0.499495, -0.709977), (-0.735014, 0.677007, 0.037632)160.23339, 162.10082, 219.29248
49generate(0.99975, 0.001013, 0.022334), (0.020927, 0.309191, -0.95077), (-0.007868, 0.950999, 0.309093)-4.61595, 196.73531, 142.44358
50generate(0.441519, -0.85543, 0.27074), (0.854611, 0.309018, -0.417311), (0.273317, 0.415628, 0.867497)-39.63808, 62.88905, 19.40197
51generate(0.421377, 0.864147, 0.275121), (-0.006571, -0.300452, 0.953774), (0.906862, -0.403706, -0.120925)-41.36216, -196.15835, 206.80591
52generate(0.448378, 0.013616, 0.89374), (-0.845621, -0.317522, 0.429074), (0.289625, -0.948153, -0.130856)-169.46424, -63.95993, 226.65642
53generate(-0.429766, -0.5402, 0.723523), (-0.861304, 0.485779, -0.148912), (-0.27103, -0.68717, -0.674047)-109.09695, 55.45251, 354.62934
54generate(-0.99949, -0.031946, -0.000297), (-0.031946, 0.999317, 0.018573), (-0.000297, 0.018573, -0.999827)56.31415, -2.94497, 413.87044
55generate(-0.473455, 0.835988, -0.277425), (0.496308, 0.5134, 0.700071), (0.727681, 0.193764, -0.657979)98.17656, -158.44903, 322.51053
56generate(-0.453659, 0.50142, 0.736731), (-0.00583, 0.825008, -0.565091), (-0.891156, -0.260653, -0.371349)-111.99674, 117.25394, 309.07914
57generate(-0.473455, 0.496308, 0.727681), (0.835988, 0.5134, 0.193764), (-0.277425, 0.700071, -0.657979)-109.56301, -63.21758, 350.36732
58generate(-0.478686, 0.512339, 0.713), (0.512339, -0.496481, 0.700725), (0.713, 0.700725, -0.024833)-106.39047, -158.22241, 191.48175
59generate(-0.462123, 0.527358, 0.712976), (-0.529505, -0.809014, 0.255189), (0.711384, -0.259596, 0.653103)-106.86348, -36.4671, 51.99688
60generate(-0.446656, 0.52061, 0.727643), (-0.849751, 0.007712, -0.527128), (-0.280039, -0.85376, 0.438944)-110.32834, 133.78664, 124.67607

-
Components

#1: Protein P1


Mass: 27296.846 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP1, RESIDUES 537-782 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#2: Protein P1


Mass: 25297.660 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP2, RESIDUES 81-310 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#3: Protein P1


Mass: 24338.451 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP3, RESIDUES 311-536 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#4: Protein P1


Mass: 8110.563 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP4, RESIDUES 1-80 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDescription: NONE

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 491997 / % possible obs: 22.9 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.44

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WS9

2ws9


Resolution: 4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.462 --
obs0.462 408137 35 %
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 0 0 5506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.2
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