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1rb8

The phiX174 DNA binding protein J in two different capsid environments.

Method: X-RAY DIFFRACTION Dmax: 104.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein

OrganismNot specified

UniProt P08767

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 60 （P31281） Small core protein × 60 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 1 （P31281） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 5 （P31281） Small core protein × 5 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 6 （P31281） Small core protein × 6 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 1 （P31281） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
6 Protein–DNA Heteromer Protein × 60 DNA 20 PDB declaration: 80-meric（80） Consistent with all polymer counts Chain F； UniProt 1–431 Not recorded Major spike protein × 20 （P31281） Small core protein × 20 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 120 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1RB8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-meric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–431（431 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGF_BPAL3
Isoform —
PDB entities 1
Chains and sequence ranges Author chain F； PDBConstruct 1–431； UniProt 1–431

Major spike protein

OrganismNot specified

UniProt P31281

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 60 （P08767） Small core protein × 60 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 1 （P08767） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 5 （P08767） Small core protein × 5 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 6 （P08767） Small core protein × 6 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 1 （P08767） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
6 Protein–DNA Heteromer Protein × 60 DNA 20 PDB declaration: 80-meric（80） Consistent with all polymer counts Chain G； UniProt 1–187 Not recorded Capsid protein × 20 （P08767） Small core protein × 20 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 120 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1RB8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M06 Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography Deposited 2002-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-meric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；318.15 K；3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Resolution 3.50 Å R-free 0.234
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å
1M0F Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy Deposited 2002-06-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM Tris and 1 mM EDTA；pH 7.5；10 mM Tris and 1 mM EDTA
Resolution 16.00 Å

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGG_BPAL3
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–187； UniProt 1–187

Small core protein

Enterobacteria phage phiX174

UniProt P69592

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 180 DNA 60 PDB declaration: 240-MERIC（240） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 60 （P08767） Major spike protein × 60 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 1 （P08767） Major spike protein × 1 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 5 （P08767） Major spike protein × 5 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 6 （P08767） Major spike protein × 6 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 1 （P08767） Major spike protein × 1 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236
6 Protein–DNA Heteromer Protein × 60 DNA 20 PDB declaration: 80-meric（80） Consistent with all polymer counts Chain J； UniProt 1–37 Not recorded Capsid protein × 20 （P08767） Major spike protein × 20 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 120 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；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 Resolution 3.50 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1RB8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC
Chain 3 2–38（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain 3 2–38（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric
Chain 3 2–38（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain 3 2–38（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain 3 2–38（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
9K3M The structure of Microviridae PJNS001 Deposited 2024-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric
Chain AC 1–38（38 aa）
Chain AF 1–38（38 aa）
Chain BA 1–38（38 aa）
Chain BD 1–38（38 aa）
Chain C 1–38（38 aa）
Chain CB 1–38（38 aa）
Chain CE 1–38（38 aa）
Chain DC 1–38（38 aa）
Chain DF 1–38（38 aa）
Chain EA 1–38（38 aa）
Chain ED 1–38（38 aa）
Chain FB 1–38（38 aa）
Chain FE 1–38（38 aa）
Chain GC 1–38（38 aa）
Chain GF 1–38（38 aa）
Chain H 1–38（38 aa）
Chain HA 1–38（38 aa）
Chain HD 1–38（38 aa）
Chain IB 1–38（38 aa）
Chain IE 1–38（38 aa）
Chain J 1–38（38 aa）
Chain JC 1–38（38 aa）
Chain JF 1–38（38 aa）
Chain KA 1–38（38 aa）
Chain KD 1–38（38 aa）
Chain L 1–38（38 aa）
Chain LB 1–38（38 aa）
Chain LE 1–38（38 aa）
Chain MC 1–38（38 aa）
Chain MF 1–38（38 aa）
Chain NA 1–38（38 aa）
Chain ND 1–38（38 aa）
Chain O 1–38（38 aa）
Chain OB 1–38（38 aa）
Chain OE 1–38（38 aa）
Chain PC 1–38（38 aa）
Chain PF 1–38（38 aa）
Chain QA 1–38（38 aa）
Chain QD 1–38（38 aa）
Chain R 1–38（38 aa）
Chain RB 1–38（38 aa）
Chain RE 1–38（38 aa）
Chain SC 1–38（38 aa）
Chain SF 1–38（38 aa）
Chain TA 1–38（38 aa）
Chain TD 1–38（38 aa）
Chain UB 1–38（38 aa）
Chain UE 1–38（38 aa）
Chain V 1–38（38 aa）
Chain VC 1–38（38 aa）
Chain VF 1–38（38 aa）
Chain WA 1–38（38 aa）
Chain WD 1–38（38 aa）
Chain XB 1–38（38 aa）
Chain XE 1–38（38 aa）
Chain Y 1–38（38 aa）
Chain YC 1–38（38 aa）
Chain YF 1–38（38 aa）
Chain ZA 1–38（38 aa）
Chain ZD 1–38（38 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；pH 7.2~7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGJ_BPPHX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J； PDBConstruct 1–37； UniProt 1–37

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1rb8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rb8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1rb8
Deposition date deposition_date2003-11-03
Structure title titleThe phiX174 DNA binding protein J in two different capsid environments.
Keywords keywords;bacteriophage alpha3, bacteriophage phiX174, bacteriophage alpha3 chimera, alpha3, phiX174, three-dimentional structure, virion, Microviridae, Icosahedral virus, Virus-DNA COMPLEX ;; Virus/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.50 Å
Radius of gyration Rg (electron density) rg_electron31.04 Å
Forward intensity I(0) i090483000.00
Molecular weight molecular_weight72731.0 kDa
Excluded volume excluded_volume89959 ų
Envelope volume envelope_volume122000 ų
Hydration-shell volume shell_volume34080 ų
Envelope diameter envelope_diameter110.6 Å
Shell Rg shell_rg36.50 Å
Envelope Rg envelope_rg31.37 Å
Shape Rg shape_rg30.96 Å
Total Rg total_rg31.74 Å
Total atoms total_atoms5112
Residues n_residues639
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.6 Å
Rg (real space) rg_real31.58 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real9.0480e+07
I(0) uncertainty (real space) i0_real_error1.3800e+06
Rg (reciprocal space) rg_reciprocal31.55 Å
I(0) (reciprocal space) i0_reciprocal90480000.0000
Solution quality estimate total_estimate0.8892
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5 Å
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12960000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1rb8f_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.1 — Microviridae-like VP
Domain ID domain_idd1rb8g_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.1 — Microviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id1rb8F00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology169 — Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
Homologous superfamily homologous superfamily10 — Microviridae F protein
Domain ID domain_id1rb8G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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8. Citations (4)

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9. Files and Curves (10)