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- PDB-1cd3: PROCAPSID OF BACTERIOPHAGE PHIX174 -

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Basic information

Entry
Database: PDB / ID: 1cd3
TitlePROCAPSID OF BACTERIOPHAGE PHIX174
Components
  • PROTEIN (CAPSID PROTEIN GPF)
  • PROTEIN (SCAFFOLDING PROTEIN GPB)
  • PROTEIN (SCAFFOLDING PROTEIN GPD)
  • PROTEIN (SPIKE PROTEIN GPG)
KeywordsVIRUS / COMPLEX (VIRUS CAPSID PROTEINS) / BACTERIOPHAGE / PROCAPSID / SCAFFOLDING PROTEIN / CHAPERONE / Icosahedral virus
Function / homology
Function and homology information


viral scaffold assembly and maintenance / viral scaffold / symbiont-mediated perturbation of host process / viral procapsid maturation / Hydrolases; Acting on peptide bonds (peptidases) / T=1 icosahedral viral capsid / viral capsid / peptidase activity / host cell cytoplasm / symbiont entry into host cell ...viral scaffold assembly and maintenance / viral scaffold / symbiont-mediated perturbation of host process / viral procapsid maturation / Hydrolases; Acting on peptide bonds (peptidases) / T=1 icosahedral viral capsid / viral capsid / peptidase activity / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / proteolysis
Similarity search - Function
Scaffolding protein gpD of bacteriophage procapsid fold / Scaffolding protein gpD of bacteriophage procapsid / Scaffold protein B / Scaffold protein B superfamily / Scaffold protein B / Procapsid Of Bacteriophage Phix174, Chain 1 / Scaffold protein D / Scaffold protein D / Scaffold protein D superfamily / Bacteriophage scaffolding protein D ...Scaffolding protein gpD of bacteriophage procapsid fold / Scaffolding protein gpD of bacteriophage procapsid / Scaffold protein B / Scaffold protein B superfamily / Scaffold protein B / Procapsid Of Bacteriophage Phix174, Chain 1 / Scaffold protein D / Scaffold protein D / Scaffold protein D superfamily / Bacteriophage scaffolding protein D / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Jelly Rolls - #20 / Few Secondary Structures / Irregular / Viral coat protein subunit / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Internal scaffolding protein B / Capsid protein F / Major spike protein G / External scaffolding protein D
Similarity search - Component
Biological speciesEnterobacteria phage phiX174 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRossmann, M.G. / Dokland, T.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.
Authors: Dokland, T. / Bernal, R.A. / Burch, A. / Pletnev, S. / Fane, B.A. / Rossmann, M.G.
#1: Journal: Nature / Year: 1997
Title: Structure of a viral procapsid with molecular scaffolding.
Authors: Dokland, T. / McKenna, R. / Ilag, L.L. / Bowman, B.R. / Incardona, N.L. / Fane, B.A. / Rossmann, M.G.
#2: Journal: Structure / Year: 1995
Title: DNA packaging intermediates of bacteriophage phi X174.
Authors: Ilang, L.L. / Olson, N.H. / Dokland, T. / Music, C.L. / Cheng, R.H. / Bowen, Z. / McKenna, R. / Rossmann, M.G. / Baker, T.S. / Incardona, N.L.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.
Authors: McKenna, R. / Ilag, L.L. / Rossmann, M.G.
#4: Journal: Nature / Year: 1992
Title: Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications.
Authors: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L.
#5: Journal: The Bacteriophages (The Viruses) / Year: 1988
Title: The Bacteriophages
#6: Journal: Nature / Year: 1977
Title: Nucleotide sequence of bacteriophage phi X174 DNA.
Authors: Sanger, F. / Air, G.M. / Barrell, B.G. / Brown, N.L. / Coulson, A.R. / Fiddes, C.A. / Hutchison, C.A. / Slocombe, P.M. / Smith, M.
History
DepositionMar 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / citation_editor / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / 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_remark.text / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
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 1.000000 0.000000 0.000000 188.08200 X0 2 0.000000 1.000000 0.000000 188.08200 X0 3 0.000000 0.000000 1.000000 188.08200 X1 1 0.834253 0.463850 -0.298103 -4.02480 X1 2 -0.298103 0.834253 0.463850 -4.02480 X1 3 0.463850 -0.298103 0.834253 -4.02480 CRYSTAL AU = (X0) * (BIOMT 1-20) * CHAINS 1,2,3,4,F,G,B + (X1) * (BIOMT 1-20) * CHAINS 1,2,3,4,F,G,B

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)


Theoretical massNumber of molelcules
Total (without water)149,1457
Polymers149,1457
Non-polymers00
Water1,72996
1
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)
x 60


Theoretical massNumber of molelcules
Total (without water)8,948,725420
Polymers8,948,725420
Non-polymers00
Water7,566420
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
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)
x 5


  • icosahedral pentamer
  • 746 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)745,72735
Polymers745,72735
Non-polymers00
Water63135
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)
x 6


  • icosahedral 23 hexamer
  • 895 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)894,87242
Polymers894,87242
Non-polymers00
Water75742
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
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)
x 20
1: PROTEIN (SCAFFOLDING PROTEIN GPD)
2: PROTEIN (SCAFFOLDING PROTEIN GPD)
3: PROTEIN (SCAFFOLDING PROTEIN GPD)
4: PROTEIN (SCAFFOLDING PROTEIN GPD)
F: PROTEIN (CAPSID PROTEIN GPF)
G: PROTEIN (SPIKE PROTEIN GPG)
B: PROTEIN (SCAFFOLDING PROTEIN GPB)
x 20


  • crystal asymmetric unit, crystal frame
  • 5.97 MDa, 280 polymers
Theoretical massNumber of molelcules
Total (without water)5,965,816280
Polymers5,965,816280
Non-polymers00
Water5,044280
TypeNameSymmetry operationNumber
transform to crystal frame2
identity operation1_555x,y,z2
point symmetry operation38
Unit cell
Length a, b, c (Å)774.000, 774.000, 774.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
PROTEIN (SCAFFOLDING PROTEIN GPD)


Mass: 16953.316 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P69486
#2: Protein PROTEIN (CAPSID PROTEIN GPF)


Mass: 48407.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03641
#3: Protein PROTEIN (SPIKE PROTEIN GPG)


Mass: 19061.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03643
#4: Protein PROTEIN (SCAFFOLDING PROTEIN GPB)


Mass: 13863.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Strain: C / References: UniProt: P03633
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 30

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Sample preparation

Crystal growMethod: vapor diffusion / pH: 6
Details: PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Dokland, T., (1998) Acta Cryst., D54, 878.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 MMES1reservoirpH6.0
243-47 %(v/v)ammonium sulfate1reservoir
315-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.5→45 Å / Num. obs: 632194 / % possible obs: 67.14 % / Observed criterion σ(I): -3 / Redundancy: 2.69 % / Rmerge(I) obs: 0.217 / Rsym value: 0.217
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.11 % / % possible all: 27.3
Reflection shell
*PLUS
% possible obs: 27.2 % / Num. unique obs: 25651 / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
MGRmodel building
X-PLOR3.851refinement
DENZOdata reduction
SnBphasing
MGRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHX

1phx


Resolution: 3.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.275 --
obs-564313 67.2 %
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9755 0 0 96 9851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.31
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.09
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.5→3.64 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.403 26288
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.31
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.09

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