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- PDB-3m8l: Crystal Structure Analysis of the Feline Calicivirus Capsid Protein -

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Basic information

Entry
Database: PDB / ID: 3m8l
TitleCrystal Structure Analysis of the Feline Calicivirus Capsid Protein
ComponentsCapsid proteinCapsid
KeywordsVIRUS / fcv-5 capsid / icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid
Similarity search - Function
Calicivirus coat protein / Calicivirus coat protein / Jelly Rolls - #20 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesFeline calicivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASE EXTENSION / Resolution: 3.4 Å
AuthorsZhou, Y. / Prasad, B.V.V.
CitationJournal: J.Virol. / Year: 2010
Title: Conformational changes in the capsid of a calicivirus upon interaction with its functional receptor
Authors: Ossiboff, R.J. / Zhou, Y. / Lightfoot, P.J. / Prasad, B.V. / Parker, J.S.
History
DepositionMar 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 28, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _cell.Z_PDB / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Sep 6, 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: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)175,7853
Polymers175,7853
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,547,080180
Polymers10,547,080180
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 879 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)878,92315
Polymers878,92315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.05 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,054,70818
Polymers1,054,70818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 15


  • crystal asymmetric unit, crystal frame
  • 2.64 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)2,636,77045
Polymers2,636,77045
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)427.080, 450.726, 467.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
6generate(1), (1), (1)
7generate(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)
8generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)
9generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
10generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
11generate(1), (1), (1)
12generate(0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5)
13generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
14generate(-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699)
15generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)

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Components

#1: Protein Capsid protein / Capsid / VP1


Mass: 58594.891 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Feline calicivirus / References: UniProt: A2T4Q0

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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 growTemperature: 298 K / pH: 7
Details: 0.45 M ammonium phosphate with Additive Screen Reagent C10 (1.0 M Glycine), pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 542590 / Observed criterion σ(I): 5

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Processing

Software
NameClassification
HKL-3000data collection
RAVEmodel building
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RAVEphasing
RefinementMethod to determine structure: PHASE EXTENSION
Starting model: PDB ENTRY 2GH8

2gh8


Resolution: 3.4→30 Å
RfactorNum. reflection
Rfree0.37 -
Rwork0.39 -
obs0.39 542590
all-542590
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12360 0 0 0 12360

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