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8v5d

Human mitochondrial DNA polymerase catalytic subunit, PolG, in an APO conformation

Method: ELECTRON MICROSCOPY Dmax: 89.0 Å Quality: EXCELLENT
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 26–1239 Mutation：D198A, E200A No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8V5D 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 oligomeric state 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 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 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: 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 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: 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
5C52 Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma Deposited 2015-06-19 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: pentameric
Chain A 25–1239（1215 aa）
Not recorded 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
5C53 Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma Deposited 2015-06-19 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: 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different experimental conditions 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 method 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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
8V5R Active conformation of DNA polymerase gamma bound to DNA Deposited 2023-11-30 Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 16–1229； UniProt 26–1239

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 8v5d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8v5d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8v5d
Deposition date deposition_date2023-11-30
Structure title titleHuman mitochondrial DNA polymerase catalytic subunit, PolG, in an APO conformation
Keywords keywords;DNA BINDING PROTEIN, DNA polymerase, mitochondrial DNA replication, DNA polymerase catalytic subunit, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.19 Å
Radius of gyration Rg (electron density) rg_electron29.05 Å
Forward intensity I(0) i0145047000.00
Molecular weight molecular_weight95073.0 kDa
Excluded volume excluded_volume118870 ų
Envelope volume envelope_volume153580 ų
Hydration-shell volume shell_volume42523 ų
Envelope diameter envelope_diameter98.3 Å
Shell Rg shell_rg37.49 Å
Envelope Rg envelope_rg29.08 Å
Shape Rg shape_rg29.09 Å
Total Rg total_rg29.74 Å
Total atoms total_atoms6694
Residues n_residues851
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 dmax89.0 Å
Rg (real space) rg_real30.01 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.4500e+08
I(0) uncertainty (real space) i0_real_error2.1980e+06
Rg (reciprocal space) rg_reciprocal30.09 Å
I(0) (reciprocal space) i0_reciprocal145100000.0000
Solution quality estimate total_estimate0.9046
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.3 Å
Skewness Skewness skewness0.109
Kurtosis Kurtosis kurtosis-0.525
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33800000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.858
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)