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1a5t

CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER COMPLEX OF ESCHERICHIA COLI DNA POLYMERASE III

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DELTA PRIME

Escherichia coli K12

UniProt P28631

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–334 Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；277 K；THE PROTEIN WAS CRYSTALLIZED FROM 20-27% PEG 400, 100 MM HEPES, PH6.8, 100 MM MGCL2, 1-3% GLYCEROL, 10MM MGSO4, AT 4C, temperature 277K Resolution 2.20 Å R-free 0.265

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 1A5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JR3 Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III Deposited 2001-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；Polyethylene glycol, ammonium sulphate, dithiothreitol, dimethylacetamide, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.70 Å R-free 0.304
1XXH ATPgS Bound E. Coli Clamp Loader Complex Deposited 2004-11-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–334（334 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.95；293 K；PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.45 Å R-free 0.350
1XXH ATPgS Bound E. Coli Clamp Loader Complex Deposited 2004-11-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–334（334 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.95；293 K；PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.45 Å R-free 0.350
1XXI ADP Bound E. coli Clamp Loader Complex Deposited 2004-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.95；293 K；PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.10 Å R-free 0.369
1XXI ADP Bound E. coli Clamp Loader Complex Deposited 2004-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.95；293 K；PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.10 Å R-free 0.369
3GLF Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.260
3GLF Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain J 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.260
3GLG Crystal Structure of a Mutant (gammaT157A) E. coli Clamp Loader Bound to Primer-Template DNA Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.25 Å R-free 0.263
3GLG Crystal Structure of a Mutant (gammaT157A) E. coli Clamp Loader Bound to Primer-Template DNA Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain J 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.25 Å R-free 0.263
3GLH Crystal Structure of the E. coli clamp loader bound to Psi Peptide Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；300 mM NaK Tartrate, 10% PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.89 Å R-free 0.361
3GLH Crystal Structure of the E. coli clamp loader bound to Psi Peptide Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；300 mM NaK Tartrate, 10% PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.89 Å R-free 0.361
3GLH Crystal Structure of the E. coli clamp loader bound to Psi Peptide Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain O 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；300 mM NaK Tartrate, 10% PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.89 Å R-free 0.361
3GLI Crystal Structure of the E. coli clamp loader bound to Primer-Template DNA and Psi Peptide Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.257
3GLI Crystal Structure of the E. coli clamp loader bound to Primer-Template DNA and Psi Peptide Deposited 2009-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain J 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.257
8GIY E. coli clamp loader with closed clamp Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8GIZ E. coli clamp loader with open clamp Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8GJ0 E. coli clamp loader with open clamp on primed template DNA (form 1) Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.
Resolution 2.90 Å
8GJ1 E. coli clamp loader with open clamp on primed template DNA (form 2) Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.
Resolution 3.00 Å
8GJ2 E. coli clamp loader with closed clamp on primed template DNA Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.
Resolution 2.60 Å
8GJ3 E. coli clamp loader on primed template DNA Deposited 2023-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.
Resolution 2.80 Å
8VAL Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8VAM Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8VAN Structure of the E. coli clamp loader bound to the beta clamp in an Initial-Binding conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
8VAP Structure of the E. coli clamp loader bound to the beta clamp in a Fully-Open conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–334（334 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8VAQ Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA1 conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8VAR Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8VAS Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8VAT Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation Deposited 2023-12-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9OYB Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 1 with flexibly bound DNA at the shoulder Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9OYC Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 2 with flexibly bound DNA at the shoulder Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
9OYD Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 3 with disordered DNA at the shoulder Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9OYE Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 1 with sharply bent DNA Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
9OYF Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 2 with less bent DNA Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9OYG Structure of the E. coli clamp loader DnaX-complex alone Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9OYH Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9OYI Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 1 with fully open clamp and unsettled DNA Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9OYJ Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 2 with fully open clamp and settled DNA Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
9OYK Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 3 with partially closed clamp Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9OYL Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 4 with fully closed clamp Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
9OYM Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 5 with fully closed clamp Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9OYN Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 6 with fully closed clamp Deposited 2025-06-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

34 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HOLB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–334； UniProt 1–334

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 1a5t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a5t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a5t
Deposition date deposition_date1998-02-18
Structure title titleCRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER COMPLEX OF ESCHERICHIA COLI DNA POLYMERASE III
Keywords keywordsZINC FINGER, DNA REPLICATION; ZINC FINGER
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_guinier24.24 Å
Radius of gyration Rg (electron density) rg_electron23.27 Å
Forward intensity I(0) i021658400.00
Molecular weight molecular_weight35731.0 kDa
Excluded volume excluded_volume44850 ų
Envelope volume envelope_volume55334 ų
Hydration-shell volume shell_volume20665 ų
Envelope diameter envelope_diameter79.6 Å
Shell Rg shell_rg29.37 Å
Envelope Rg envelope_rg23.04 Å
Shape Rg shape_rg23.26 Å
Total Rg total_rg24.09 Å
Total atoms total_atoms3063
Residues n_residues324
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 dmax78.8 Å
Rg (real space) rg_real24.31 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real2.1660e+07
I(0) uncertainty (real space) i0_real_error3.1500e+05
Rg (reciprocal space) rg_reciprocal24.29 Å
I(0) (reciprocal space) i0_reciprocal21660000.0000
Solution quality estimate total_estimate0.8945
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3790000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.967
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1a5ta1
Class classa — All alpha proteins
Fold Fold folda.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamilya.80.1 — post-AAA+ oligomerization domain-like
Family Family familya.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain
Domain ID domain_idd1a5ta2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (3 domains)

Domain ID domain_id1a5tA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1a5tA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id1a5tA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily10 —
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8. Citations (2)

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9. Files and Curves (10)