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- PDB-1al0: PROCAPSID OF BACTERIOPHAGE PHIX174 -

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Basic information

Entry
Database: PDB / ID: 1al0
TitlePROCAPSID OF BACTERIOPHAGE PHIX174
Components
  • CAPSID PROTEIN GPF
  • SCAFFOLDING PROTEIN GPB
  • SCAFFOLDING PROTEIN GPD
  • 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 / modulation by virus 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 / modulation by virus 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 / Viral coat protein subunit / Few Secondary Structures / Irregular / 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: 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.
#1: Journal: Structure / Year: 1995
Title: DNA Packaging Intermediates of Bacteriophage Phi X174
Authors: Ilag, 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.
#2: 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.
#3: 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.
#4: Journal: The Bacteriophages (The Viruses) / Year: 1988
Title: Biology of the Bacteriophage PhiX174
Authors: Hayashi, M. / Aoyama, A. / Delwood, L. / Richardson, D.L. / Hayashi, M.N.
#5: 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, J.C. / Hutchison, C.A. / Slocombe, P.M. / Smith, M.
History
DepositionJun 6, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details
Revision 1.4Apr 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: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB


Theoretical massNumber of molelcules
Total (without water)149,1617
Polymers149,1617
Non-polymers00
Water00
1
1: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB
x 60


Theoretical massNumber of molelcules
Total (without water)8,949,685420
Polymers8,949,685420
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
1: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB
x 5


  • icosahedral pentamer
  • 746 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)745,80735
Polymers745,80735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB
x 6


  • icosahedral 23 hexamer
  • 895 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)894,96842
Polymers894,96842
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
1: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB
x 20
1: SCAFFOLDING PROTEIN GPD
2: SCAFFOLDING PROTEIN GPD
3: SCAFFOLDING PROTEIN GPD
4: SCAFFOLDING PROTEIN GPD
F: CAPSID PROTEIN GPF
G: SPIKE PROTEIN GPG
B: SCAFFOLDING PROTEIN GPB
x 20


  • crystal asymmetric unit, crystal frame
  • 5.97 MDa, 280 polymers
Theoretical massNumber of molelcules
Total (without water)5,966,456280
Polymers5,966,456280
Non-polymers00
Water0
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
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 CAPSID PROTEIN GPF


Mass: 48423.375 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 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 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 22

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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
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
210 mMTris1drop
30.25 M1dropNaCl
45 mMEDTA1drop
55 mM1dropMgCl2
642-47 %satammonium sulfate1reservoir
70.1 MMES1reservoir

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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: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.5→45 Å / Num. obs: 527445 / % possible obs: 55.3 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.247 / Rsym value: 0.247
Reflection
*PLUS
Num. all: 1072459 / Num. measured all: 1646040

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(AGROVATAdata scaling
SCALAdata scaling
X-PLOR3.1phasing
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 / σ(F): 2 /
RfactorNum. reflection
Rwork0.316 -
obs0.316 459892
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9524 0 0 0 9524
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.5→3.64 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.393 8377
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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