[English] 日本語
Yorodumi
- PDB-2vf1: X-ray crystallographic structure of the picobirnavirus capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vf1
TitleX-ray crystallographic structure of the picobirnavirus capsid
ComponentsCAPSID PROTEIN
KeywordsVIRUS / DSRNA VIRUS STRUCTURE / VIRAL PROTEIN / PICOBIRNAVIRUS / CAPSID PROTEIN / TRIACONTAHEDRON
Function / homology
Function and homology information


Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #120 / N-terminal domain of TfIIb - #440 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3350 / : / : / Picobirnavirus, Capsid protein / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / N-terminal domain of TfIIb / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #120 / N-terminal domain of TfIIb - #440 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3350 / : / : / Picobirnavirus, Capsid protein / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / N-terminal domain of TfIIb / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet / Helix non-globular / Special / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRABBIT PICOBIRNAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsDuquerroy, S. / Da Costa, B. / Vigouroux, A. / Lepault, J. / Navaza, J. / Delmas, B. / Rey, F.A.
CitationJournal: Embo J. / Year: 2009
Title: The Picobirnavirus Crystal Structure Provides Functional Insights Into Virion Assembly and Cell Entry.
Authors: Duquerroy, S. / Da Costa, B. / Henry, C. / Vigouroux, A. / Libersou, S. / Lepault, J. / Navaza, J. / Delmas, B. / Rey, F.A.
History
DepositionOct 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 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: CAPSID PROTEIN
B: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)116,8942
Polymers116,8942
Non-polymers00
Water93752
1
A: CAPSID PROTEIN
B: CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)7,013,618120
Polymers7,013,618120
Non-polymers00
Water2,162120
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: CAPSID PROTEIN
B: CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 584 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)584,46810
Polymers584,46810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAPSID PROTEIN
B: CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 701 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)701,36212
Polymers701,36212
Non-polymers00
Water21612
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)407.424, 407.424, 808.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309017, -0.705526, -0.637762), (0.70552, 0.619743, -0.343745), (0.63777, -0.343731, 0.689274)287.84998, 228.55669, 206.60377
3generate(-0.809017, -0.436046, -0.394151), (0.436028, 0.004474, -0.899922), (0.394171, -0.899913, 0.186509)83.7836, 502.26796, 454.03041
4generate(-0.809017, 0.436028, 0.394171), (-0.436046, 0.004474, -0.899913), (-0.394151, -0.899922, 0.186509)-330.18634, 442.87415, 400.34471
5generate(0.309017, 0.70552, 0.63777), (-0.705526, 0.619743, -0.343731), (-0.637762, -0.343745, 0.689274)-381.96745, 132.45548, 119.73848
6generate(-1, 2.2E-5, -6.0E-6), (2.2E-5, 0.844886, -0.534946), (-6.0E-6, -0.534946, -0.844886)-136.2171, 126.8387, 437.42683
7generate(-0.309005, 0.705543, 0.63775), (0.254918, 0.707474, -0.659164), (-0.91626, -0.041111, -0.398469)-424.0633, 209.42757, 140.60275
8generate(0.809024, 0.436052, 0.39413), (0.157516, 0.485176, -0.860112), (-0.566276, 0.757933, 0.323834)-219.9924, 308.31784, -214.86408
9generate(0.80901, -0.436022, -0.394192), (-0.157577, 0.4852, -0.860087), (0.56628, 0.757935, 0.323824)193.97656, 286.84653, -137.73058
10generate(-0.309029, -0.705504, -0.637782), (-0.254914, 0.707513, -0.659124), (0.916253, -0.041109, -0.398484)245.75254, 174.68626, 265.40737
11generate(-1, 1.8E-5, 6.3E-5), (1.8E-5, -0.844886, 0.534946), (6.3E-5, 0.534946, 0.844886)-136.22497, 578.86656, -167.84452
12generate(-0.308964, 0.705516, 0.637799), (-0.254905, -0.707503, 0.659138), (0.916277, 0.041071, 0.398433)-424.0578, 496.28939, 128.99578
13generate(0.80905, 0.43599, 0.394147), (-0.157549, -0.485194, 0.860096), (0.56623, -0.757958, -0.323856)-219.97089, 397.39083, 484.45111
14generate(0.808984, -0.436085, -0.394176), (0.157545, -0.485182, 0.860103), (-0.566325, -0.75791, -0.323802)193.99459, 418.84532, 407.29429
15generate(-0.30907, -0.70553, -0.637733), (0.254926, -0.707484, 0.65915), (-0.916236, 0.041148, 0.39852)245.75241, 531.00349, 4.15342
16generate(1, -4.1E-5, -5.6E-5), (-4.1E-5, -1), (-5.6E-5, -1)0.02193, 705.69973, 269.57464
17generate(0.308952, -0.705532, -0.637787), (-0.705532, -0.619714, 0.343771), (-0.637787, 0.343771, -0.689238)287.85098, 477.13134, 62.95465
18generate(-0.809057, -0.435996, -0.394125), (-0.435996, -0.004457, 0.899938), (-0.394125, 0.899938, -0.186486)83.75954, 203.42836, -184.46049
19generate(-0.808977, 0.436079, 0.394197), (0.436079, -0.004492, 0.899897), (0.394197, 0.899897, -0.186531)-330.20495, 262.839, -130.75146
20generate(0.309082, 0.705514, 0.637745), (0.705514, -0.619772, 0.343705), (0.637745, 0.343705, -0.68931)-381.95765, 573.25977, 149.85768
21generate(2.1E-5, -0.960442, 0.278479), (0.278459, -0.267459, -0.922457), (0.960448, 0.077565, 0.267438)233.25361, 590.52629, 136.78404
22generate(-0.499999, -0.690964, 0.522082), (-0.690964, -0.045139, -0.721478), (0.522082, -0.721478, -0.454862)71.27906, 418.96813, 486.23065
23generate(-0.309029, -0.254914, 0.916253), (-0.705504, 0.707513, -0.041109), (-0.637782, -0.659124, -0.398484)-122.70588, 60.69704, 377.63714
24generate(0.309017, -0.254898, 0.916262), (0.254934, 0.950358, 0.178405), (-0.916252, 0.178456, 0.358659)-80.62063, 10.83148, -38.92396
25generate(0.50002, -0.690938, 0.522096), (0.863056, 0.347792, -0.366298), (0.071509, 0.633755, 0.770222)139.37444, 338.28396, -187.77936
26generate(-4.4E-5, -0.960436, 0.278502), (-0.278459, 0.267498, 0.922445), (-0.960448, -0.07751, -0.267454)233.24384, 115.16396, 132.77746
27generate(-0.5, -0.690922, 0.522137), (0.690985, 0.045168, 0.721457), (-0.522054, 0.721517, 0.454832)71.25658, 286.7287, -216.66003
28generate(-0.308964, -0.254905, 0.916277), (0.705516, -0.707503, 0.041071), (0.637799, 0.659138, 0.398433)-122.7077, 645.00768, -108.05558
29generate(0.309058, -0.254946, 0.916234), (-0.254947, -0.950348, -0.178442), (0.916234, -0.178442, -0.358711)-80.59695, 694.87152, 308.50314
30generate(0.499981, -0.690988, 0.522067), (-0.863077, -0.347764, 0.366277), (-0.071537, -0.633716, -0.770251)139.3932, 367.4101, 457.34615

-
Components

#1: Protein CAPSID PROTEIN


Mass: 58446.816 Da / Num. of mol.: 2 / Fragment: MATURE CHAIN, RESIDUES 66-590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RABBIT PICOBIRNAVIRUS / Strain: R5-9 / Description: ISOLATED FROM RABBIT FAECAL MATERIAL / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9Q1V2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNIPROT SEQUENCE Q9Q1V2 HAS AN UNKNOWN RESIDUE AT POSITION 179 DEFINED FOR ENTRY VERSION 18

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 8.49 Å3/Da / Density % sol: 85.61 %
Description: LOW RESOLUTIONS PHASES OBTAINED BY MR USING AN ELECTRON MICROSCOPY MAP AT 20 A RES. PHASE EXTENSION WITH 30-FOLD NON CRYSTALLOGRAPHIC SYMMETRY CORRESPONDING TO HALF A CAPSID IN THE ASYMMETRIC UNIT.
Crystal growDetails: AMMONIUMSULFATE 1M TRIS 0.1M PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.006
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 3.4→80 Å / Num. obs: 736678 / % possible obs: 70 % / Observed criterion σ(I): -2 / Redundancy: 1.5 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 2.6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.2 / % possible all: 41.6

-
Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ELECTRON MICROSCOPY MAP AT 20 ANG RESOLUTION

Resolution: 3.4→49.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 16444870.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3738 5 %RESOLUTION SHELLS
Rwork0.273 ---
obs0.273 736678 70 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.04 Å20 Å20 Å2
2--7.04 Å20 Å2
3----14.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 3.4→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8234 0 0 52 8286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
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
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 267 3 %
Rwork0.371 76302 -
obs--43.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

+
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