5c53

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

Method: X-RAY DIFFRACTION D_max: 133.6 Å Quality: REASONABLE

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

DNA polymerase subunit gamma-1

Homo sapiens

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	Pol gamma B × 2 DNA (26-MER) × 1 ;DNA (5'-D(APAPAPAPCPGPAPGPGPGPCPCPAPGPTPGPCPCPGPTPAPC)-3') ; × 1 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

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 5C53	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 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 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 ligand/ion 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
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

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	5c53
Deposition date deposition_date	2015-06-19
Structure title title	Probing 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, mitochondrial toxicity, drug efficacy and toxicity, TRANSFERASE, transferase-dna complex ;; transferase/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	41.12 Å
Radius of gyration Rg (electron density) rg_electron	40.94 Å
Forward intensity I(0) i0	705539000.00
Molecular weight molecular_weight	208760.0 kDa
Excluded volume excluded_volume	257390 Å³
Envelope volume envelope_volume	365580 Å³
Hydration-shell volume shell_volume	72204 Å³
Envelope diameter envelope_diameter	148.3 Å
Shell Rg shell_rg	47.87 Å
Envelope Rg envelope_rg	40.74 Å
Shape Rg shape_rg	40.95 Å
Total Rg total_rg	41.25 Å
Total atoms total_atoms	14634
Residues n_residues	1751
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	133.6 Å
Rg (real space) rg_real	41.06 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	7.0550e+08
I(0) uncertainty (real space) i0_real_error	1.2940e+07
Rg (reciprocal space) rg_reciprocal	41.12 Å
I(0) (reciprocal space) i0_reciprocal	705600000.0000
Solution quality estimate total_estimate	0.5874
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.2 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	124800000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 0.993; Sysdev: 0.008; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	DNA polymerase subunit gamma-1
Molecular weight formula_weight	135989.5 kDa
EC 编号 ec_number	2.7.7.7
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	14634

WVSSSVPASDPSDGQRRRQQQPQQPQVLSSEGGQLRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTRYGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTGASSPTQRDWQEQLVVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPAISSWDWLDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLESAGVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEAEAKMENLRAAVPGQPLALTARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDEGEWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRSQPGP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 2 Entity 2 polymer

Description description	Pol gamma B
Molecular weight formula_weight	102458.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MRSRVAVRACHKVCRCLLSGFGGRVDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSLLSGCHPGFGPLGVELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRKLRENLLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPRTSNQWLDFWLRHRLQWWRKFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVSKLHGRDGRKNVVPCVLSVNGDLDRGMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQGLFNELLENGISVWPGYLETMQSSLEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYISSAKNVMRSRVAVRACHKVCRCLLSGFGGRVDAGQPELLTERSSPKGGHVKSHAELEGNGEHPEAPGSGEGSEALLEICQRRHFLSGSKQQLSRDSLLSGCHPGFGPLGVELRKNLAAEWWTSVVVFREQVFPVDALHHKPGPLLPGDSAFRLRENLLHGALEHYVNCLDLVNKRLPYGLAQIGVCFHPVFDTKQIRNGVKSIGEKTEASLVWFTPPRTSNQWLDFWLRHRLQWWRKFAMSPSNFSSSDCQDEEGRKGNKLYYNFPWGKELIETLWNLGDHELLHMYPGNVSKLHGRDGRKNVVPCVLSVNGDLDRGMLAYLYDSFQLTENSFTRKKNLHRKVLKLHPCLAPIKVALDVGRGPTLELRQVCQGLFNELLENGISVWPGYLETMQSSLEQLYSKYDEMSILFTVLVTETTLENGLIHLRSRDTTMKEMMHISKLKDFLIKYISSAKNV

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 3 Entity 3 polymer

Description description	DNA (26-MER)
Molecular weight formula_weight	7955.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AGCGATACGGCACTGGCCCTCGTTTT

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(APAPAPAPCPGPAPGPGPGPCPCPAPGPTPGPCPCPGPTPAPC)-3') ;
Molecular weight formula_weight	6795.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

AAAACGAGGGCCAGTGCCGTAC

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	;[[(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 ;
Molecular weight formula_weight	489.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	291.2 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5c53B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	5c53B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	5c53C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	5c53C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	217.447 Å
Unit-cell length b length_b	217.447 Å
Unit-cell length c length_c	163.593 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.567 Å
Low-resolution limit resolution_low	48.909 Å
R factor r_factor	0.3014
R_work r_work	0.2998
R_free r_free	0.3382

fit	/app/data/saxs_computation/c5/5c53/5c53.fit
pddf	/app/data/pr_computation/c5/5c53/5c53.pr.out
profile	/app/data/saxs_computation/c5/5c53/5c53.dat

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

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

DNA polymerase subunit gamma-1

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 (7)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)