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- PDB-1b35: CRICKET PARALYSIS VIRUS (CRPV) -

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Basic information

Entry
Database: PDB / ID: 1b35
TitleCRICKET PARALYSIS VIRUS (CRPV)
Components
  • PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
  • PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
  • PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
  • PROTEIN (CRICKET PARALYSIS VIRUS, VP4)
KeywordsVIRUS / INSECT PICORNA-LIKE VIRUS / Icosahedral virus
Function / homology
Function and homology information


viral capsid / host cell cytoplasm / structural molecule activity
Similarity search - Function
Cricket Paralysis Virus, Vp4; Chain D / Cricket Paralysis Virus, Vp4; Chain D / Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein ...Cricket Paralysis Virus, Vp4; Chain D / Cricket Paralysis Virus, Vp4; Chain D / Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesCricket paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTate, J.G. / Liljas, L. / Scotti, P.D. / Christian, P.D. / Lin, T.W. / Johnson, J.E.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of cricket paralysis virus: the first view of a new virus family.
Authors: Tate, J. / Liljas, L. / Scotti, P. / Christian, P. / Lin, T. / Johnson, J.E.
History
DepositionDec 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 19, 2014Group: Other / Version format compliance
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
B: PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
C: PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
D: PROTEIN (CRICKET PARALYSIS VIRUS, VP4)


Theoretical massNumber of molelcules
Total (without water)95,4124
Polymers95,4124
Non-polymers00
Water3,207178
1
A: PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
B: PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
C: PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
D: PROTEIN (CRICKET PARALYSIS VIRUS, VP4)
x 60


Theoretical massNumber of molelcules
Total (without water)5,724,750240
Polymers5,724,750240
Non-polymers00
Water4,324240
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: PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
B: PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
C: PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
D: PROTEIN (CRICKET PARALYSIS VIRUS, VP4)
x 5


  • icosahedral pentamer
  • 477 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)477,06220
Polymers477,06220
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
B: PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
C: PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
D: PROTEIN (CRICKET PARALYSIS VIRUS, VP4)
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)572,47524
Polymers572,47524
Non-polymers00
Water43224
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
6
A: PROTEIN (CRICKET PARALYSIS VIRUS, VP1)
B: PROTEIN (CRICKET PARALYSIS VIRUS, VP2)
C: PROTEIN (CRICKET PARALYSIS VIRUS, VP3)
D: PROTEIN (CRICKET PARALYSIS VIRUS, VP4)
x 15


  • crystal asymmetric unit, crystal frame
  • 1.43 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,431,18760
Polymers1,431,18760
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)330.000, 334.000, 395.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)
3generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5)
4generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)
5generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)
6generate(-1), (1), (-1)
7generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)
8generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)
9generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)
10generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)
11generate(-1), (-1), (1)
12generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)
13generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)
14generate(0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699)
15generate(0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5)
DetailsTHE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE ASYMMETRIC UNIT. IT MAY BE GENERATED USING THE MTRIX TRANSFORMATIONS BELOW. ALSO SEE REMARKS 295 AND 300.

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Components

#1: Protein PROTEIN (CRICKET PARALYSIS VIRUS, VP1) / CRPV


Mass: 28853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cricket paralysis virus / Genus: Cripavirus / References: UniProt: P13418
#2: Protein PROTEIN (CRICKET PARALYSIS VIRUS, VP2) / CRPV


Mass: 28709.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cricket paralysis virus / Genus: Cripavirus / References: UniProt: P13418
#3: Protein PROTEIN (CRICKET PARALYSIS VIRUS, VP3) / CRPV


Mass: 31917.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cricket paralysis virus / Genus: Cripavirus / References: UniProt: P13418
#4: Protein PROTEIN (CRICKET PARALYSIS VIRUS, VP4) / CRPV


Mass: 5932.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cricket paralysis virus / Genus: Cripavirus / References: UniProt: P13418
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA SALT BRIDGE IS VISIBLE IN ELECTRON DENSITY MAPS, BETWEEN RESIDUES ARG A 222 AND GLU A 112 FROM AN ...A SALT BRIDGE IS VISIBLE IN ELECTRON DENSITY MAPS, BETWEEN RESIDUES ARG A 222 AND GLU A 112 FROM AN ADJACENT, 5-FOLD RELATED COPY OF VP1.

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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

Crystal growpH: 6
Details: VIRUS STORED AT 10MG/ML IN 200MM NAH2PO4, PH7.2. WELL SOLUTION CONSISTED OF 8% (W/V) MPEG 5K, 50MM LI2SO4, 50MM MES, PH6.0.
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlvirus1drop
2200 mMsodium phosphate1drop
38 %(w/v)mPEG50001reservoir
450 mM1reservoirLi2SO4
550 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 7, 1997 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 210945 / % possible obs: 25.2 % / Observed criterion σ(I): 2 / Redundancy: 1.23 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.06 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 5 / % possible all: 9.2
Reflection
*PLUS
Num. measured all: 312272 / Rmerge(I) obs: 0.128

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PLV

2plv


Resolution: 2.4→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high rms absF: 10511948.71 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: RESIDUES B 253 - B 271 ARE PRESENT IN THE MODEL, BUT THE SEQUENCE OF THESE RESIDUES DOES NOT CORRESPOND TO ANY PREDICTED SEQUENCE IN THE VIRAL GENOME. THEY ARE INCLUDED ONLY TO PARTIALLY ...Details: RESIDUES B 253 - B 271 ARE PRESENT IN THE MODEL, BUT THE SEQUENCE OF THESE RESIDUES DOES NOT CORRESPOND TO ANY PREDICTED SEQUENCE IN THE VIRAL GENOME. THEY ARE INCLUDED ONLY TO PARTIALLY MODEL THE POOR QUALITY, APPARENTLY HELICAL DENSITY ON THE VIRUS SURFACE AT THE CAPSID 2-FOLD AXES.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 11742 5.6 %SPHERES
Rwork0.228 ---
obs0.228 209358 25.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.36 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 0 178 6892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
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
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 677 4.2 %
Rwork0.289 15318 -
obs--11.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.289

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