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2bpa

ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS

Method: X-RAY DIFFRACTION Dmax: 105.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

Enterobacteria phage phiX174

UniProt P03641

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 1； UniProt 1–426 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 1； UniProt 1–426 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain 1； UniProt 1–426 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain 1； UniProt 1–426 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 1； UniProt 1–426 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å

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 2BPA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain F 1–426（426 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-MERIC
Chain A 1–426（426 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；50 mM Sodium tetraborate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–426（426 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；50 mM Sodium tetraborate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–426（426 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；50 mM Sodium tetraborate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–426（426 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；50 mM Sodium tetraborate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–426（426 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；50 mM Sodium tetraborate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 27.00 Å

3 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGF_BPPHX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain 1； PDBConstruct 1–426； UniProt 1–426

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

Enterobacteria phage phiX174

UniProt P03643

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 2； UniProt 1–175 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 2； UniProt 1–175 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain 2； UniProt 1–175 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain 2； UniProt 1–175 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 2； UniProt 1–175 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å

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 2BPA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å
1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1999-03-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric
Chain G 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION
Resolution 3.50 Å

2 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGG_BPPHX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain 2； PDBConstruct 1–175； UniProt 1–175

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

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 3； UniProt 2–38 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03643） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
2 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 3； UniProt 2–38 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
3 Protein–DNA Heteromer Protein × 15 DNA 5 PDB declaration: eicosameric（20） Consistent with all polymer counts Chain 3； UniProt 2–38 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03643） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
4 Protein–DNA Heteromer Protein × 18 DNA 6 PDB declaration: 24-meric（24） Consistent with all polymer counts Chain 3； UniProt 2–38 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03643） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å
5 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain 3； UniProt 2–38 Not recorded ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å

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 2BPA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC
Chain J 1–37（37 aa）
Not recorded 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
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain J 1–37（37 aa）
Not recorded 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
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric
Chain J 1–37（37 aa）
Not recorded 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
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain J 1–37（37 aa）
Not recorded 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
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain J 1–37（37 aa）
Not recorded 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
1RB8 The phiX174 DNA binding protein J in two different capsid environments. Deposited 2003-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Heteromer；Protein × 60 PDB declaration: 80-meric
Chain J 1–37（37 aa）
Not recorded 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
9K3M The structure of Microviridae PJNS001 Deposited 2024-10-19 Different construct Different mutation/modification Different oligomeric state 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGJ_BPPHX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain 3； PDBConstruct 1–37； UniProt 2–38

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 2bpa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bpa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bpa
Deposition date deposition_date1991-12-03
Structure title titleATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS
Keywords keywordsPROTEIN-DNA COMPLEX, SINGLE STRAND, 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_guinier32.10 Å
Radius of gyration Rg (electron density) rg_electron31.60 Å
Forward intensity I(0) i086739100.00
Molecular weight molecular_weight72634.0 kDa
Excluded volume excluded_volume90507 ų
Envelope volume envelope_volume126310 ų
Hydration-shell volume shell_volume34566 ų
Envelope diameter envelope_diameter111.0 Å
Shell Rg shell_rg37.00 Å
Envelope Rg envelope_rg32.15 Å
Shape Rg shape_rg31.54 Å
Total Rg total_rg32.29 Å
Total atoms total_atoms5120
Residues n_residues642
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 dmax105.1 Å
Rg (real space) rg_real32.17 Å
Rg uncertainty (real space) rg_real_error0.87 Å
I(0) (real space) i0_real8.6740e+07
I(0) uncertainty (real space) i0_real_error1.4530e+06
Rg (reciprocal space) rg_reciprocal32.14 Å
I(0) (reciprocal space) i0_reciprocal86740000.0000
Solution quality estimate total_estimate0.6862
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3 Å
Skewness Skewness skewness0.353
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10580000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.976; Smooth: 0.896
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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_idd2bpa1_
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_idd2bpa2_
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_id2bpa100
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_id2bpa200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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8. Citations (6)

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9. Files and Curves (10)