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- PDB-1ijs: CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.... -

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Basic information

Entry
Database: PDB / ID: 1ijs
TitleCPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C
Components
  • DNA (5'-D(*AP*C)-3')
  • DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
  • PROTEIN (PARVOVIRUS COAT PROTEIN)
KeywordsVirus/DNA / MUTANT A300D / VIRAL COAT PROTEIN / COMPLEX (PARVOVIRUS COAT PROTEIN-DNA) / Icosahedral virus / Virus-DNA COMPLEX
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / host cell / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus ...permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / host cell / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA / Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesCanine parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsLlamas-Saiz, A.L. / Agbandje-McKenna, M. / Parker, J.S.L. / Wahid, A.T.M. / Parrish, C.R. / Rossmann, M.G.
Citation
Journal: Virology / Year: 1996
Title: Structural analysis of a mutation in canine parvovirus which controls antigenicity and host range.
Authors: Llamas-Saiz, A.L. / Agbandje-McKenna, M. / Parker, J.S. / Wahid, A.T. / Parrish, C.R. / Rossmann, M.G.
#1: Journal: Virology / Year: 1993
Title: Structure, Sequence, and Function Correlations Among Parvoviruses
Authors: Chapman, M.S. / Rossmann, M.G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Determination and Refinement of the Canine Parvovirus Empty-Capsid Structure
Authors: Wu, H. / Keller, W. / Rossmann, M.G.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of Monoclinic Canine Parvovirus
Authors: Tsao, J. / Chapman, M.S. / Wu, H. / Agbandje, M. / Keller, W. / Rossmann, M.G.
#4: Journal: Science / Year: 1991
Title: The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W.
History
DepositionSep 12, 1996Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2011Group: Structure summary
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 285THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 0.453521 0.200253 0.868416 0.00000 X0 2 -0.716194 0.661791 0.221396 0.00000 X0 3 -0.530360 -0.722416 0.443592 0.00000 CRYSTAL AU = (X0) * (BIOMT 1-60) * CHAINS P,N,A

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
A: DNA (5'-D(*AP*C)-3')
P: PROTEIN (PARVOVIRUS COAT PROTEIN)


Theoretical massNumber of molelcules
Total (without water)67,9713
Polymers67,9713
Non-polymers00
Water0
1
N: DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
A: DNA (5'-D(*AP*C)-3')
P: PROTEIN (PARVOVIRUS COAT PROTEIN)
x 60


Theoretical massNumber of molelcules
Total (without water)4,078,249180
Polymers4,078,249180
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
N: DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
A: DNA (5'-D(*AP*C)-3')
P: PROTEIN (PARVOVIRUS COAT PROTEIN)
x 5


  • icosahedral pentamer
  • 340 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)339,85415
Polymers339,85415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
N: DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
A: DNA (5'-D(*AP*C)-3')
P: PROTEIN (PARVOVIRUS COAT PROTEIN)
x 6


  • icosahedral 23 hexamer
  • 408 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)407,82518
Polymers407,82518
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
N: DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3')
A: DNA (5'-D(*AP*C)-3')
P: PROTEIN (PARVOVIRUS COAT PROTEIN)
x 60


  • crystal asymmetric unit, crystal frame
  • 4.08 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,078,249180
Polymers4,078,249180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
identity operation1_555x,y,z1
point symmetry operation59
Unit cell
Length a, b, c (Å)267.600, 268.500, 274.300
Angle α, β, γ (deg.)61.90, 62.60, 60.20
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: DNA chain DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') / DNA FRAGMENT OF CANINE PARVOVIRUS


Mass: 2629.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus / Strain: STRAIN D
#2: DNA chain DNA (5'-D(*AP*C)-3') / DNA FRAGMENT OF CANINE PARVOVIRUS


Mass: 557.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus / Strain: D
#3: Protein PROTEIN (PARVOVIRUS COAT PROTEIN)


Mass: 64783.629 Da / Num. of mol.: 1 / Mutation: A300D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus / Strain: STRAIN D / Cell line: CANINE (CANIS FAMILIARIS) A72 / Species (production host): Canis lupus / Cell line (production host): CANINE A72 / Production host: Canis lupus familiaris (dog) / Strain (production host): familiaris / Keywords: MUTANT A300D / References: UniProt: P30129, UniProt: P17455*PLUS

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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: 7.5
Details: 0.75% PEG8000, 10MM TRIS-HCL, 8MM CACL2.2H2O, PH=7.5
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 800011
3BIS-TRIS-PROPANE_HCL11
4CACL211
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Tsao, J., (1992) Acta Crystallogr.,Sect.B, 48, 75.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.75 %PEG80001reservoir
26 mM1reservoirCaCl2
310 mMTris-HCl1reservoirpH7.5
41

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.5→15 Å / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.0896
Reflection
*PLUS
Highest resolution: 3.25 Å / Observed criterion σ(I): 3 / Redundancy: 1.2 %

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Processing

Software
NameVersionClassification
PURDUESOFTWAREdata collection
PURDUESOFTWAREdata reduction
PURDUEAVERAGING PROGRAMmodel building
refinement
PURDUEDATA PROCESSING PACKAGEdata scaling
PURDUEAVERAGING PROGRAMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CANINE PARVOVIRUS (MONOCLINIC P21)

Highest resolution: 3.25 Å
Details: INTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, SUGGESTING THAT ONE IN FIVE OF THE N-TERMINI IS ON THE OUTSIDE OF THE CAPSID, AND THAT THE ...Details: INTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, SUGGESTING THAT ONE IN FIVE OF THE N-TERMINI IS ON THE OUTSIDE OF THE CAPSID, AND THAT THE POLYPEPTIDE RUNS DOWN THE FIVE-FOLD AXIS TO JOIN RESIDUE 37 ON THE INSIDE SURFACE (SEE ACTA CRYSTALLOGR. 1992 REFERENCE ABOVE). ELEVEN NUCLEOTIDES OF THE GENOMIC SINGLE-STRANDED DNA ARE BOUND TO EACH OF THE 60 PROTOMERS OF THE CAPSID, TOGETHER CONSTITUTING 13 PERCENT OF THE GENOME. THE ELECTRON DENSITY IS THE AVERAGE OF UP TO 60 DIFFERENT REGIONS OF THE DNA SEQUENCE. THUS, THE ELECTRON DENSITY FOR EACH BASE IS EXPECTED TO BE BLURRED AS IT IS THE AVERAGE OF MANY BASES. HOWEVER, FOR MANY OF THE NUCLEOTIDES, THE ELECTRON DENSITY IS DISTINCTIVE FOR PURINE OR PYRIMIDINE, AND IN SOME CASES FOR INDIVIDUAL BASE-TYPE. THIS SHOWS THAT THERE IS SOME SEQUENCE PREFERENCE. THERE ARE 30+ REGIONS OF THE ENCAPSIDATED GENOMIC SEQUENCE THAT SATISFY THIS PREFERENCE (SEE *JRNL* REFERENCE), BUT THE HOMOLOGY BETWEEN THEM IS WEAK. THE BASE-TYPES OF THE DNA MODEL WERE CHOSEN TO FIT THE ELECTRON DENSITY AND STERIC CONSTRAINTS BEST, AND IS THEREFORE SIMILAR TO THE CONSENSUS OF THE VIRAL SEQUENCES THAT BIND. NOTE THAT THE SEQUENCE OF THE DNA IN THE GENBANK ENTRY PVCPVC IS THE NEGATIVE OF THE SEQUENCE THAT IS ENCAPSIDATED IN THE VIRION. INTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, SUGGESTING THAT ONE IN FIVE OF THE N-TERMINI IS ON THE OUTSIDE OF THE CAPSID, AND THAT THE POLYPEPTIDE RUNS DOWN THE FIVE-FOLD AXIS TO JOIN RESIDUE 37 ON THE INSIDE SURFACE (SEE ACTA CRYSTALLOGR. 1992 REFERENCE ABOVE).
Refinement stepCycle: LAST / Highest resolution: 3.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 218 0 0 4571
Refinement
*PLUS
Highest resolution: 3.25 Å / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

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