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- PDB-2vf1: X-ray crystallographic structure of the picobirnavirus capsid -

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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 / 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 ...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 / 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
Uncharacterized protein
Similarity search - Component
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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