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- PDB-1rb8: The phiX174 DNA binding protein J in two different capsid environ... -

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Basic information

Entry
Database: PDB / ID: 1rb8
TitleThe phiX174 DNA binding protein J in two different capsid environments.
Components
  • Capsid protein
  • DNA (5'-D(P*CP*AP*AP*A)-3')
  • Major spike protein
  • Small core protein
KeywordsVirus/DNA / bacteriophage alpha3 / bacteriophage phiX174 / bacteriophage alpha3 chimera / alpha3 / phiX174 / three-dimentional structure / virion / Microviridae / Icosahedral virus / Virus-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Microvirus J protein-like / Microvirus J 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 ...Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Microvirus J protein-like / Microvirus J 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA / Capsid protein F / Major spike protein G / DNA-binding protein J
Similarity search - Component
Biological speciesEnterobacteria phage phiX174 (virus)
Enterobacteria phage alpha3 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBernal, R.A. / Hafenstein, S. / Esmeralda, R. / Fane, B.A. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells.
Authors: Bernal, R.A. / Hafenstein, S. / Esmeralda, R. / Fane, B.A. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Structural Studies of Bacteriophage Alpha3 Assembly
Authors: Bernal, R.A. / Hafenstein, S. / Olson, N.H. / Bowman, V.D. / Chipman, P.R. / Baker, T.S. / Fane, B.A. / Rossmann, M.G.
#2: 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.
#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.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 400COMPOUND THE VIRUS IS A CHIMERA. THE CAPSID PROTEIN F AND THE SPIKE PROTEIN G ARE FROM ALPHA3 BUT ...COMPOUND THE VIRUS IS A CHIMERA. THE CAPSID PROTEIN F AND THE SPIKE PROTEIN G ARE FROM ALPHA3 BUT THE J PROTEIN WAS REPLACED BY THE J PROTEIN OF PHIX174.
Remark 999SEQUENCE RESIDUE 160 OF THE F PROTEIN IS AN ARG ACCORDING TO THE REPORTED SEQUENCE BUT NO DENSITY ...SEQUENCE RESIDUE 160 OF THE F PROTEIN IS AN ARG ACCORDING TO THE REPORTED SEQUENCE BUT NO DENSITY IS SEEN FOR THE SIDE CHAIN IN THE CRYSTAL STRUCTURE FOR THIS RESIDUE. AFTER A STRUCTURAL SEQUENCE ALIGNMENT WITH HOMOLOGOUS BACTERIOPHAGES PHIX174 AND G4, RESIDUE 160 WAS FOUND TO BE A GLYCINE IN THE OTHER PHAGES. CONSEQUENTLY, THE AUTHORS STATE RESIDUE 160 SHOULD BE A GLYCINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Capsid protein
G: Major spike protein
J: Small core protein
X: DNA (5'-D(P*CP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,02810
Polymers74,1854
Non-polymers1,8436
Water00
1
F: Capsid protein
G: Major spike protein
J: Small core protein
X: DNA (5'-D(P*CP*AP*AP*A)-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,561,687600
Polymers4,451,096240
Non-polymers110,591360
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
F: Capsid protein
G: Major spike protein
J: Small core protein
X: DNA (5'-D(P*CP*AP*AP*A)-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 380 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)380,14150
Polymers370,92520
Non-polymers9,21630
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
F: Capsid protein
G: Major spike protein
J: Small core protein
X: DNA (5'-D(P*CP*AP*AP*A)-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 456 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)456,16960
Polymers445,11024
Non-polymers11,05936
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
F: Capsid protein
G: Major spike protein
J: Small core protein
X: DNA (5'-D(P*CP*AP*AP*A)-3')
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.52 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,520,562200
Polymers1,483,69980
Non-polymers36,864120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)295.143, 295.143, 678.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.33260137, -0.68192639, 0.65142359), (0.82957107, 0.54009122, 0.14182167), (-0.44854008, 0.49323213, 0.74534139)
3generate(-0.74727233, -0.27380906, 0.6054854), (0.66034782, -0.20405687, 0.72270439), (-0.07432943, 0.93988798, 0.33329521)
4generate(-0.74727234, 0.6603477, -0.07432956), (-0.27380897, -0.20405691, 0.93988796), (0.60548556, 0.72270435, 0.33329527)
5generate(0.33260134, 0.829571, -0.44854011), (-0.68192638, 0.54009116, 0.49323209), (0.65142367, 0.14182163, 0.74534148)
6generate(-0.84349524, -0.4292161, -0.32293863), (-0.42921602, 0.17712992, 0.88566277), (-0.32293858, 0.8856628, -0.33363467)
7generate(-0.49176202, 0.18410211, -0.85104437), (-0.39307122, 0.82519738, 0.40564054), (0.77695895, 0.5339997, -0.33343536)
8generate(0.37089258, 0.015015, -0.92855432), (0.3718778, 0.91380244, 0.1633157), (0.85096744, -0.40588129, 0.33333896)
9generate(0.55230922, -0.70280479, -0.44835234), (0.80849751, 0.32049594, 0.49357293), (-0.20319033, -0.63509659, 0.74522882)
10generate(-0.19822373, -0.9773547, -0.07406126), (0.3133943, -0.13479272, 0.94000796), (-0.92870415, 0.16312155, 0.33301646)
11generate(0.29293887, -0.22731525, 0.92871663), (-0.22731531, -0.96003505, -0.16328035), (0.92871663, -0.16328031, -0.33290383)
12generate(-0.50770891, 0.13553916, 0.85080001), (-0.79878491, -0.4440293, -0.40593194), (0.32276051, -0.8857015, 0.33370424)
13generate(-0.43804322, 0.83906551, 0.32262529), (-0.45195407, 0.1046775, -0.88587821), (-0.77708148, -0.53386486, 0.33336572)
14generate(0.40566034, 0.91101431, 0.07411198), (0.33386877, -0.07220879, -0.93984971), (-0.8508651, 0.40600332, -0.33345156)
15generate(0.85743211, 0.25195475, 0.44869702), (0.47270316, -0.73023732, -0.49325968), (0.20337611, 0.63503718, -0.74522878)
16generate(-0.44944363, 0.65653135, -0.605778), (0.65653134, -0.21709487, -0.72238241), (-0.60577805, -0.72238249, -0.3334615)
17generate(0.66686956, 0.36228512, -0.65117922), (0.36228506, -0.92125929, -0.14153027), (-0.65117938, -0.14153033, -0.74561027)
18generate(0.81442297, -0.58027145, 0.00044362), (-0.58027155, -0.81442307, -0.00014187), (0.00044347, -0.00014183, -1)
19generate(-0.21069721, -0.86855722, 0.44856992), (-0.86855731, -0.04423025, -0.49361118), (0.44856987, -0.49361109, -0.74507254)
20generate(-0.99180972, -0.10417105, 0.07390436), (-0.10417108, 0.32493889, -0.93998038), (0.07390438, -0.93998036, -0.33312916)

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Components

#1: Protein Capsid protein / F protein / GPF


Mass: 49294.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: wt alpha3 capsid protein F / Source: (natural) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P08767
#2: Protein Major spike protein / G protein / GPG


Mass: 19598.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: wt alpha3 spike protein G / Source: (natural) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P31281
#3: Protein/peptide Small core protein / J protein


Mass: 4107.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Gene: J / Production host: Escherichia coli (E. coli) / Strain (production host): recA- cells / References: UniProt: P69592
#4: DNA chain DNA (5'-D(P*CP*AP*AP*A)-3')


Mass: 1183.845 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical
ChemComp-DC / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 307.197 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N3O7P / Comment: dCMP*YM

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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 / Method: vapor diffusion, sitting drop / pH: 5
Details: 4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2sodium citrate11
3glycerol11
4sodium azide11
5beta-mercapto-ethanol11
6NaCl11
7water11
8PEG 800012
9sodium citrate12
10glycerol12
11NaCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→500 Å / Num. all: 342669 / Num. obs: 269234 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 1 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 3.5→3.66 Å / Rmerge(I) obs: 0.157 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SnBphasing
ENVELOPEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacteriophage alpha3 wild-type structure

Resolution: 3.5→92.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 112625.55 / Data cutoff high rms absF: 112625.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: the O3*-P bond between residue (X A 3 ) and Residue (X A 4 ) is 1.91A. The density for the nucleic acid in this region is very weak and therefore difficult to interpret.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 13533 5 %RANDOM
Rwork0.234 ---
all0.234 342669 --
obs0.234 269234 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.312307 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.28 Å24.11 Å20 Å2
2---3.28 Å20 Å2
3---6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.44 Å
Luzzati sigma a0.43 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.5→92.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 120 0 0 5112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.66 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 1737 5.3 %
Rwork0.308 30983 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP

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