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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P03007 New Search
11PDB entries
18Biological assembly
18chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1J53 Structure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA Polymerase III at pH 8.5 Deposited 2002-01-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–186（186 aa） Fragment：N-terminal exonuclease domain (residues 1-186)
Not recorded MN MANGANESE (II) ION × 2 TMP THYMIDINE-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, magnesium sulfate, cacodylate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.227
1J54 Structure of the N-terminal exonuclease domain of the epsilon subunit of E.coli DNA polymerase III at pH 5.8 Deposited 2002-01-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–186（186 aa） Fragment：N-terminal exonuclease domain (residues 1-186)
Not recorded MN MANGANESE (II) ION × 2 TMP THYMIDINE-5'-PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；PEG 8000, magnesium sulfate, cacodylate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.70 Å R-free 0.234
2GUI Structure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit of E. coli DNA Polymerase III Deposited 2006-04-30 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 2–186（185 aa） Fragment：N-terminal exonuclease domain, residues 2-186
Not recorded MN MANGANESE (II) ION × 2 U5P URIDINE-5'-MONOPHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.1 M Cacodylate Acid, 20% PEG-8K, 2.5 mM UMP, 5 mM MnSO4, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.60 Å R-free 0.197
2IDO Structure of the E. coli Pol III epsilon-Hot proofreading complex Deposited 2006-09-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–186（186 aa） Fragment：exonuclease domain
Not recorded MN MANGANESE (II) ION × 2 TMP THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Crystals grown in .1M Tris, 5mM MnSO4, 5mM dTMP, and 22% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.244
2IDO Structure of the E. coli Pol III epsilon-Hot proofreading complex Deposited 2006-09-15 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 1–186（186 aa） Fragment：exonuclease domain
Not recorded MN MANGANESE (II) ION × 3 TMP THYMIDINE-5'-PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；Crystals grown in .1M Tris, 5mM MnSO4, 5mM dTMP, and 22% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.244
2XY8 Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III Deposited 2010-11-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–186（186 aa） Fragment：EXONUCLEASE DOMAIN, RESIDUES 1-186
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Pressure 1
Resolution not provided
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 209–243（35 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 209–243（35 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 209–243（35 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 209–243（35 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 1.70 Å R-free 0.246
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 200–243（44 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 200–243（44 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 200–243（44 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04 Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 200–243（44 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation：L66P,L66P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.15 Å R-free 0.291
5FKU cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain D 1–243（243 aa）
Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.34 Å
5FKV cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain D 1–243（243 aa）
Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.04 Å
5FKW cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon) Deposited 2015-10-20 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
Chain D 1–243（243 aa）
Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 7.30 Å
5M1S Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode Deposited 2016-10-10 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain D 1–243（243 aa）
Mutation：T183L M185L A186P F187L No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Prior to sample preparation 0.1 volumes of 0.05% Tween 20 were added to the sample 3 microliters were pipetted onto the grid and blotted for 4 seconds
Resolution 6.70 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.