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- PDB-2gh8: X-ray structure of a native calicivirus -

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Basic information

Entry
Database: PDB / ID: 2gh8
TitleX-ray structure of a native calicivirus
ComponentsCapsid proteinCapsid
KeywordsVIRUS / native calicivirus / vesivirus / icosahedral T=3 capsid / domain swapping / N-terminal arm / shell domain / protruding domain / icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm
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 speciesSan Miguel sea lion virus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: X-ray structure of a native calicivirus: Structural insights into antigenic diversity and host specificity.
Authors: Chen, R. / Neill, J.D. / Estes, M.K. / Prasad, B.V.
History
DepositionMar 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHOR MAINTAINS THAT THE SEQUENCE IN THE SEQUENCE DATABSE IS INCORRECT. THESE ...SEQUENCE THE AUTHOR MAINTAINS THAT THE SEQUENCE IN THE SEQUENCE DATABSE IS INCORRECT. THESE ADDITIONAL RESIDUES SHOULD ALSO BE PRESENT IN THE SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)184,9353
Polymers184,9353
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,096,092180
Polymers11,096,092180
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
  • 925 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)924,67415
Polymers924,67415
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
  • 1.11 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,109,60918
Polymers1,109,60918
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
6
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • crystal asymmetric unit, crystal frame
  • 925 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)924,67415
Polymers924,67415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)457.553, 457.553, 457.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
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)

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Components

#1: Protein Capsid protein / Capsid / Coat protein


Mass: 61644.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) San Miguel sea lion virus 4 / Genus: Vesivirus / Species: Vesicular exanthema of swine virus / Strain: serotype 4 / References: UniProt: P36285

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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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 0.8M ammonium sulfate, 1M lithium sulfate, 0.1M trisodium citrate dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2002 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 248269 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.469 / % possible all: 84.7

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALEPACKdata scaling
RAVEmodel building
CNS1.1refinement
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYOEM STRUCTURE OF SAN MIGUEL SEA LION VIRUS AT A RESOLUTION OF 19 ANGSTROM

Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 22363 10 %RANDOM
Rwork0.249 ---
obs0.249 223124 86.1 %-
all-259113 --
Displacement parametersBiso mean: 54.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12747 0 0 0 12747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0107
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_deg1.414
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.445
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9747
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: 3.2→3.31 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3732 1636 10 %
Rwork0.367 15118 -
obs--65.14 %

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