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5c52

Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma

Method: X-RAY DIFFRACTION Dmax: 135.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase subunit gamma-1

Homo sapiens

UniProt P54098

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 × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts Chain A； UniProt 25–1239 Not recorded DNA polymerase subunit gamma-2, mitochondrial × 2 （Q9UHN1） DNA (26-MER) × 1 ;DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3') ; × 1 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；PEG4000, KCl, HEPES Resolution 3.64 Å R-free 0.314

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 5C52 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IKM Crystal structure of human mitochondrial DNA polymerase holoenzyme Deposited 2009-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–1239（1170 aa） Fragment：UNP residues 70-1239
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION
Resolution 3.24 Å R-free 0.303
3IKM Crystal structure of human mitochondrial DNA polymerase holoenzyme Deposited 2009-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–1239（1170 aa） Fragment：UNP residues 70-1239
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION
Resolution 3.24 Å R-free 0.303
4ZTU Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Deposited 2015-05-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 30–1239（1210 aa） Fragment：UNP residues 30-1239
Mutation：D198A, E200A MG MAGNESIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；PEG8000, KCl, CaCl2
Resolution 3.30 Å R-free 0.316
4ZTZ Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Deposited 2015-05-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 30–1239（1210 aa） Fragment：UNP residues 30-1239
Not recorded MG MAGNESIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；PEG8000, KCl, CaCl2
Resolution 3.44 Å R-free 0.320
5C51 Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma Deposited 2015-06-19 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 25–1239（1215 aa）
Not recorded MG MAGNESIUM ION × 2 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；PEG4000, KCl, HEPES
Resolution 3.43 Å R-free 0.345
5C53 Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma Deposited 2015-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 25–1239（1215 aa）
Not recorded MG MAGNESIUM ION × 2 4Y3 [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；PEG4000, KCl, HEPES
Resolution 3.57 Å R-free 0.338
8D33 Human mitochondrial DNA polymerase gamma ternary complex with GC basepair Deposited 2022-05-31 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8D37 Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in replication conformer Deposited 2022-05-31 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8D3R Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in intermediate conformer Deposited 2022-06-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8D42 Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (composite) Deposited 2022-06-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded CA CALCIUM ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8G5I Cryo-EM structure of the Mismatch Sensing Complex (I) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris, pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8G5J Cryo-EM structure of the Mismatch Uncoupling Complex (II) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
8G5K Cryo-EM structure of the Wedge Alignment Complex (VIII) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8G5L Cryo-EM structure of the Primer Separation Complex (IX) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8G5M Cryo-EM structure of the Mismatch Locking Complex (III) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8G5N Cryo-EM structure of the Guide loop Engagement Complex (VI) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
8G5O Cryo-EM structure of the Guide loop Engagement Complex (IV) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
8G5P Cryo-EM structure of the Guide loop Engagement Complex (V) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8T7E Cryo-EM structure of the Backtracking Initiation Complex (VII) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-06-20 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris, pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8UDK Human Mitochondrial DNA Polymerase gamma R853A Ternary Complex Deposited 2023-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A, R853A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM MES (pH 6.0), 150 mM NaCl, 10 mM CaCl2, 50 mM BME, 3% PEG 8000, 1-8% sucrose, 2% Jeffamine, 0.8 M NDSB
Resolution 3.43 Å R-free 0.234
8UDL Human Mitochondrial DNA Polymerase Gamma Binary Complex Deposited 2023-09-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1239（1239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.37 Å
8V54 Engaged conformation of the human mitochondrial DNA polymerase gamma bound to DNA Deposited 2023-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8V55 Human mitochondrial DNA polymerase gamma bound to a replication fork in an open conformation Deposited 2023-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8V5D Human mitochondrial DNA polymerase catalytic subunit, PolG, in an APO conformation Deposited 2023-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–1239（1214 aa）
Mutation：D198A, E200A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8V5R Active conformation of DNA polymerase gamma bound to DNA Deposited 2023-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：D198A, E200A MG MAGNESIUM ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GGB Structure of the G848S mutant of human mitochondrial DNA polymerase gamma in complex with PZL-A Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：G848S CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 A1IK1 1-[(4S)-8-chloranyl-3,4-dihydro-2H-chromen-4-yl]-3-(1-phenylpyrazol-3-yl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
9GGC Structure of the G848S mutant of human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：G848S CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å
9GGD Structure of the A467T mutant of human mitochondrial DNA polymerase gamma in complex with PZL-A Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：A467T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 A1IK1 1-[(4S)-8-chloranyl-3,4-dihydro-2H-chromen-4-yl]-3-(1-phenylpyrazol-3-yl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.67 Å
9GGE Structure of the A467T mutant of human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Mutation：A467T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9GGF Structure of WT human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9IC1 Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in replication conformer Deposited 2025-02-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9IC3 Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite) Deposited 2025-02-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 26–1239（1214 aa）
Not recorded CA CALCIUM ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9Y4C Strand displacement state I of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different construct 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 × 3 PDB declaration: tetrameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9Y4D Strand displacement state II of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different construct 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 × 3 PDB declaration: tetrameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Y4E Strand displacement state III of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different construct 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 × 3 PDB declaration: tetrameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9Y4F Strand displacement state IV of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different construct 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 × 3 PDB declaration: tetrameric
Chain A 1–1239（1239 aa）
Mutation：D198A, E200A CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å

35 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOG1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1205； UniProt 25–1239

DNA polymerase subunit gamma-2, mitochondrial

Homo sapiens

UniProt Q9UHN1

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 × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts Chain B； UniProt 1–485 Chain C； UniProt 1–485 Not recorded DNA polymerase subunit gamma-1 × 1 （P54098） DNA (26-MER) × 1 ;DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3') ; × 1 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；PEG4000, KCl, HEPES Resolution 3.64 Å R-free 0.314

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 5C52 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2G4C Crystal Structure of human DNA polymerase gamma accessory subunit Deposited 2006-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；10%PEG 8000, 100 mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Resolution 3.15 Å R-free 0.285
2G4C Crystal Structure of human DNA polymerase gamma accessory subunit Deposited 2006-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 26–485（460 aa）
Chain D 26–485（460 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；10%PEG 8000, 100 mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Resolution 3.15 Å R-free 0.285
3IKL Crystal structure of Pol gB delta-I4. Deposited 2009-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–146（146 aa）
Chain A 181–485（305 aa）
Chain B 1–146（146 aa）
Chain B 181–485（305 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION
Resolution 3.10 Å R-free 0.294
3IKM Crystal structure of human mitochondrial DNA polymerase holoenzyme Deposited 2009-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 59–485（427 aa） Fragment：UNP residues 59-485
Chain C 59–485（427 aa） Fragment：UNP residues 59-485
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION
Resolution 3.24 Å R-free 0.303
3IKM Crystal structure of human mitochondrial DNA polymerase holoenzyme Deposited 2009-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 59–485（427 aa） Fragment：UNP residues 59-485
Chain F 59–485（427 aa） Fragment：UNP residues 59-485
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION
Resolution 3.24 Å R-free 0.303
4ZTU Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Deposited 2015-05-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded MG MAGNESIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；PEG8000, KCl, CaCl2
Resolution 3.30 Å R-free 0.316
4ZTZ Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Deposited 2015-05-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded MG MAGNESIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；PEG8000, KCl, CaCl2
Resolution 3.44 Å R-free 0.320
5C51 Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma Deposited 2015-06-19 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded MG MAGNESIUM ION × 2 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；PEG4000, KCl, HEPES
Resolution 3.43 Å R-free 0.345
8D33 Human mitochondrial DNA polymerase gamma ternary complex with GC basepair Deposited 2022-05-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8D37 Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in replication conformer Deposited 2022-05-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8D3R Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in intermediate conformer Deposited 2022-06-01 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8D42 Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (composite) Deposited 2022-06-01 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8G5I Cryo-EM structure of the Mismatch Sensing Complex (I) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris, pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8G5J Cryo-EM structure of the Mismatch Uncoupling Complex (II) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
8G5K Cryo-EM structure of the Wedge Alignment Complex (VIII) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8G5L Cryo-EM structure of the Primer Separation Complex (IX) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8G5M Cryo-EM structure of the Mismatch Locking Complex (III) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8G5N Cryo-EM structure of the Guide loop Engagement Complex (VI) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
8G5O Cryo-EM structure of the Guide loop Engagement Complex (IV) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
8G5P Cryo-EM structure of the Guide loop Engagement Complex (V) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-02-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris-Hcl pH 7.9, 100 mM Nacl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8T7E Cryo-EM structure of the Backtracking Initiation Complex (VII) of Human Mitochondrial DNA Polymerase Gamma Deposited 2023-06-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM Tris, pH 7.9, 100 mM NaCl, 10 mM DTT, and 2 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8UDK Human Mitochondrial DNA Polymerase gamma R853A Ternary Complex Deposited 2023-09-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；100 mM MES (pH 6.0), 150 mM NaCl, 10 mM CaCl2, 50 mM BME, 3% PEG 8000, 1-8% sucrose, 2% Jeffamine, 0.8 M NDSB
Resolution 3.43 Å R-free 0.234
8UDL Human Mitochondrial DNA Polymerase Gamma Binary Complex Deposited 2023-09-28 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.37 Å
8V54 Engaged conformation of the human mitochondrial DNA polymerase gamma bound to DNA Deposited 2023-11-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8V55 Human mitochondrial DNA polymerase gamma bound to a replication fork in an open conformation Deposited 2023-11-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8V5R Active conformation of DNA polymerase gamma bound to DNA Deposited 2023-11-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Not recorded MG MAGNESIUM ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GGB Structure of the G848S mutant of human mitochondrial DNA polymerase gamma in complex with PZL-A Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 A1IK1 1-[(4S)-8-chloranyl-3,4-dihydro-2H-chromen-4-yl]-3-(1-phenylpyrazol-3-yl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
9GGC Structure of the G848S mutant of human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å
9GGD Structure of the A467T mutant of human mitochondrial DNA polymerase gamma in complex with PZL-A Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 A1IK1 1-[(4S)-8-chloranyl-3,4-dihydro-2H-chromen-4-yl]-3-(1-phenylpyrazol-3-yl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.67 Å
9GGE Structure of the A467T mutant of human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9GGF Structure of WT human mitochondrial DNA polymerase gamma Deposited 2024-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9IBX Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer Deposited 2025-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9IBZ Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in human-like error-editing conformer (composite) Deposited 2025-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
9IC0 Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in mouse-like error-editing conformer (composite) Deposited 2025-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 26–485（460 aa）
Chain C 26–485（460 aa）
Mutation：A169T Mutation：A169T CA CALCIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
9Y4C Strand displacement state I of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9Y4D Strand displacement state II of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Y4E Strand displacement state III of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9Y4F Strand displacement state IV of Human mitochondrial DNA polymerase gamma ternary complex Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–485（485 aa）
Chain C 1–485（485 aa）
Not recorded CA CALCIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å

36 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOG2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–485； UniProt 1–485 Author chain C； PDBConstruct 1–485； UniProt 1–485

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 5c52

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5c52
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5c52
Deposition date deposition_date2015-06-19
Structure title titleProbing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma
Keywords keywords;Nucleoside reverse transcriptase inhibitors (NRTIs), HIV reverse transcriptase (RT), human mitochondrial DNA polymerase, transferase-DNA complex ;; transferase/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_guinier41.04 Å
Radius of gyration Rg (electron density) rg_electron40.86 Å
Forward intensity I(0) i0706016000.00
Molecular weight molecular_weight208840.0 kDa
Excluded volume excluded_volume257510 ų
Envelope volume envelope_volume363890 ų
Hydration-shell volume shell_volume72155 ų
Envelope diameter envelope_diameter147.6 Å
Shell Rg shell_rg47.76 Å
Envelope Rg envelope_rg40.53 Å
Shape Rg shape_rg40.87 Å
Total Rg total_rg41.17 Å
Total atoms total_atoms14639
Residues n_residues1751
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 dmax135.6 Å
Rg (real space) rg_real40.98 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real7.0600e+08
I(0) uncertainty (real space) i0_real_error1.1310e+07
Rg (reciprocal space) rg_reciprocal41.04 Å
I(0) (reciprocal space) i0_reciprocal706100000.0000
Solution quality estimate total_estimate0.8833
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary132.0 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha128400000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.876
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5c52B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id5c52B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id5c52C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id5c52C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
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8. Citations (1)

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9. Files and Curves (10)