8uh7

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

Method: X-RAY DIFFRACTION D_max: 124.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sliding-clamp-loader small subunit

Tequatrovirus

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 × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain A； UniProt 1–187	Not recorded	Sliding-clamp-loader large subunit × 4 （P04526） Sliding clamp × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl	Resolution 2.63 Å R-free 0.244

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 8UH7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 2–187（186 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain K 2–187（186 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U60 Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog Deposited 2011-10-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 2–187（186 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K	Resolution 3.34 Å R-free 0.282
3U61 Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP Deposited 2011-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 2–187（186 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.305
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–187（187 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain Q 1–187（187 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UNF Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Deposited 2023-10-18	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–187（187 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8UNH Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Deposited 2023-10-19	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 A 1–187（187 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LOADS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–187； UniProt 1–187

Sliding-clamp-loader large subunit

Tequatrovirus

UniProt P04526

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 × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain B； UniProt 1–319 Chain C； UniProt 1–319 Chain D； UniProt 1–319 Chain E； UniProt 1–319	Not recorded	Sliding-clamp-loader small subunit × 1 （P04527） Sliding clamp × 3 （P04525） Template DNA strand × 1 Primer DNA strand × 1 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl	Resolution 2.63 Å R-free 0.244

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8UH7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain L 1–319（319 aa） Chain M 1–319（319 aa） Chain N 1–319（319 aa） Chain O 1–319（319 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U60 Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K	Resolution 3.34 Å R-free 0.282
3U61 Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP Deposited 2011-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.305
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Mutation：D110C Mutation：D110C Mutation：D110C Mutation：D110C	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain K 1–319（319 aa） Chain L 1–319（319 aa） Chain M 1–319（319 aa） Chain N 1–319（319 aa）	Mutation：D110C Mutation：D110C Mutation：D110C Mutation：D110C	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UNF Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Deposited 2023-10-18	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8UNH Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Deposited 2023-10-19	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 B 1–319（319 aa） Chain C 1–319（319 aa） Chain D 1–319（319 aa） Chain E 1–319（319 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LOADL_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–324； UniProt 1–319 Author chain C； PDBConstruct 6–324； UniProt 1–319 Author chain D； PDBConstruct 6–324； UniProt 1–319 Author chain E； PDBConstruct 6–324； UniProt 1–319

Sliding clamp

Tequatrovirus

UniProt P04525

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 × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain F； UniProt 1–228 Chain G； UniProt 1–228 Chain H； UniProt 1–228	Non-standard monomer：Yes (specific site not provided by mmCIF)	Sliding-clamp-loader small subunit × 1 （P04527） Sliding-clamp-loader large subunit × 4 （P04526） Template DNA strand × 1 Primer DNA strand × 1 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl	Resolution 2.63 Å R-free 0.244

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8UH7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZD CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4 Deposited 1999-09-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；60 mM PIPES 200 mM CASO4 0.1 % 1,4 Dioxane 15% Glycerol 15% PEG MME 5000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.259
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain P 1–228（228 aa） Chain Q 1–228（228 aa） Chain R 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U60 Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog Deposited 2011-10-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K	Resolution 3.34 Å R-free 0.282
3U61 Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP Deposited 2011-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.305
6DRT Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4 Deposited 2018-06-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350	Resolution 2.12 Å R-free 0.240
7D7D CryoEM structure of gp45-dependent transcription activation complex Deposited 2020-10-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain G 1–228（228 aa） Chain H 1–228（228 aa） Chain I 1–228（228 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain R 1–228（228 aa） Chain S 1–228（228 aa） Chain T 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UNF Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Deposited 2023-10-18	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8UNH Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Deposited 2023-10-19	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 × 8 PDB declaration: octameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9E5Y T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1 Deposited 2024-10-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
9EA2 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 2 Deposited 2024-11-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9EA3 T4 bacteriophage replicative holoenzyme containing triple mutations D75R, Q430E, and K432E in the exonuclease-deficient polymerase Deposited 2024-11-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
9EA6 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 3 Deposited 2024-11-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	CA CALCIUM ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLAMP_BPT4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–228； UniProt 1–228 Author chain G； PDBConstruct 1–228； UniProt 1–228 Author chain H； PDBConstruct 1–228； UniProt 1–228

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8uh7
Deposition date deposition_date	2023-10-07
Structure title title	Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog
Keywords keywords	Clamp loader, T4, AAA+ATPase, REPLICATION, REPLICATION-DNA complex; REPLICATION/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.95 Å
Radius of gyration Rg (electron density) rg_electron	40.77 Å
Forward intensity I(0) i0	1966420000.00
Molecular weight molecular_weight	237090.0 kDa
Excluded volume excluded_volume	225620 Å³
Envelope volume envelope_volume	427310 Å³
Hydration-shell volume shell_volume	83534 Å³
Envelope diameter envelope_diameter	137.7 Å
Shell Rg shell_rg	49.13 Å
Envelope Rg envelope_rg	40.05 Å
Shape Rg shape_rg	40.82 Å
Total Rg total_rg	40.97 Å
Total atoms total_atoms	17766
Residues n_residues	2168
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	124.0 Å
Rg (real space) rg_real	40.78 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.9660e+09
I(0) uncertainty (real space) i0_real_error	3.3270e+07
Rg (reciprocal space) rg_reciprocal	40.95 Å
I(0) (reciprocal space) i0_reciprocal	1967000000.0000
Solution quality estimate total_estimate	0.8273
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.396
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	163600000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Sliding-clamp-loader small subunit
Molecular weight formula_weight	21391.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17800

MSLFKDDIQLNEHQVAWYSKDWTAVQSAADSFKEKAENEFFEIIGAINNKTKCSIAQKDYSKFMVENALSQFPECMPAVYAMNLIGSGLSDEAHFNYLMAAVPRGKRYGKWAKLVEDSTEVLIIKLLAKRYQVNTNDAINYKSILTKNGKLPLVLKELKGLVTDDFLKEVTKNVKEQKQLKKLALEW

来源 Source

来源生物 organism	Tequatrovirus
NCBI Class编号 ncbi_taxonomy_id	10663
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Sliding-clamp-loader large subunit
Molecular weight formula_weight	36189.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,E

GPGGSMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCKIDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSSKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAANTELHLAYLFIQLACEMQWK

来源 Source

来源生物 organism	Tequatrovirus
NCBI Class编号 ncbi_taxonomy_id	10663
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Sliding clamp
Molecular weight formula_weight	25162.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H

MKLSKDTTALLKNFATINSGIMLKSGQFIMTRAVNGTTYAEANISDVIDFDVAIYDLNGFLGILSLVNDDAEISQSEDGNIKIADARSTIFWPAADPSTVVAPNKPIPFPVASAVTEIKAEDLQQLLRVSRGLQIDTIAITVKEGKIVINGFNKVEDSALTRVKYSLTLGDYDGENTFNFIINMANMKMQPGNYKLLLWAKGKQGAAKFEGEHANYVVALEADSTHDF

来源 Source

来源生物 organism	Tequatrovirus
NCBI Class编号 ncbi_taxonomy_id	10663
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Template DNA strand
Molecular weight formula_weight	9172.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TTTTTTTTTTTATGTACTCGTAGTGTCTGC

Entity 5 Entity 5 polymer

Description description	Primer DNA strand
Molecular weight formula_weight	6136.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

GCAGACACTACGAGTACATA

Entity 6 Entity 6 non-polymer

Description description	;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ;
Molecular weight formula_weight	492.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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8. Citations (1)

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Unit-cell length a length_a	93.351 Å
Unit-cell length b length_b	118.325 Å
Unit-cell length c length_c	132.882 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.628 Å
Low-resolution limit resolution_low	49.649 Å
R factor r_factor	0.1952
R_work r_work	0.1934
R_free r_free	0.2445

fit	/app/data/saxs_computation/uh/8uh7/8uh7.fit
pddf	/app/data/pr_computation/uh/8uh7/8uh7.pr.out
profile	/app/data/saxs_computation/uh/8uh7/8uh7.dat

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sliding-clamp-loader small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Sliding-clamp-loader large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)