4ebd

Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

Method: X-RAY DIFFRACTION D_max: 80.3 Å Quality: GOOD

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

DNA polymerase iota

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 26–445	Fragment：UNP residues 26-445	5'-D(PAPGPGPAPCPCP(DOC))-3' × 1 5'-D(PCPTPGPGPGPTPCPCPT)-3' × 1 0OJ South-methanocarba-2'-deoxyadenosine triphosphate × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.57 Å R-free 0.263

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 4EBD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T3N Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP Deposited 2004-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 27–414（388 aa） Chain B 27–414（388 aa）	Not recorded	MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.286
2ALZ Ternary Complex of hPoli with DNA and dCTP Deposited 2005-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 25–414（390 aa）	Not recorded	MG MAGNESIUM ION × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% PEG 5K MME, 0.4 M Ammonium Sulfate, 0.1 M MES buffer, pH 6.5, hanging drop, pH 6.50	Resolution 2.50 Å R-free 0.272
2DPI Ternary complex of hPoli with DNA and dCTP Deposited 2006-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa） Fragment：residues 1-420	Not recorded	MG MAGNESIUM ION × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.278
2DPJ structure of hPoli with DNA and dTTP Deposited 2006-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa） Fragment：residues 1-420	Not recorded	MG MAGNESIUM ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.277
2FLL Ternary complex of human DNA polymerase iota with DNA and dTTP Deposited 2006-01-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa）	Not recorded	MG MAGNESIUM ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.277
2FLN binary complex of catalytic core of human DNA polymerase iota with DNA (template A) Deposited 2006-01-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.279
2FLP Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G) Deposited 2006-01-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.276
2KHU Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota Deposited 2009-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 676–715（40 aa） Fragment：UNP residues 304-357, 676-715	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；25 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1-4 mM [U-100% 13C; U-100% 15N] D2O-1, 1-4 mM [U-100% 13C; U-100% 15N] H2O-2, 100% D2O \| 100% D2O	Resolution not provided
2KHW Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex Deposited 2009-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 676–715（40 aa） Fragment：UNP residues 304-357, 676-715	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1 mM [U-100% 15N] entity_1-1, 4 mM entity_2-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 15N] entity_1-3, 3 mM [U-100% 15N] entity_2-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] entity_1-5, 3 mM [U-100% 13C; U-100% 15N] entity_2-6, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-7, 4 mM entity_2-8, 100% D2O \| 100% D2O	Resolution not provided
2KTF Solution NMR structure of human polymerase iota UBM2 in complex with ubiquitin Deposited 2010-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 679–707（29 aa） Fragment：Ubiquitin biding motif UBM2	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；301 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 3.5 mM peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.5 mM protein, 0.5 mM [U-100% 13C; U-100% 15N] peptide, 20 mM sodium phosphate, 30 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L0F Solution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin Deposited 2010-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 674–715（42 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.18；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 5 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
2L0G Solution NMR structure of ubiquitin-binding motif (UBM2) of human polymerase iota Deposited 2010-07-01	Different construct 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 679–707（29 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.18；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] UBM2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 516–555（40 aa） Fragment：UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O \| 100% D2O	Resolution not provided
3EPG Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine Deposited 2008-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa） Fragment：Catalytic Fragment (UNP residues 1-420)	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.50 Å R-free 0.283
3EPI Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine and incoming TTP Deposited 2008-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–420（420 aa） Fragment：Catalytic Fragment (UNP residues 1-420)	Not recorded	NA SODIUM ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.90 Å R-free 0.282
3G6V DNA synthesis across an abasic lesion by human DNA polymerase-iota Deposited 2009-02-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–420（420 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals grew over a period of one day, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.251
3G6X Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position Deposited 2009-02-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–420（420 aa）	Not recorded	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.08 Å R-free 0.265
3G6Y Ternary complex of DNA Polymerase iota:DNA:dTTP with an abasic site at the templating position Deposited 2009-02-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–420（420 aa）	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.253
3GV5 Human DNA polymerase iota in complex with T template DNA and incoming ddADP Deposited 2009-03-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 GOL GLYCEROL × 1 ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；15% PEG 3350, 0.15 M CaCl2, 5% glycerol, 0.005M DTT, pH 7.5, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.253
3GV5 Human DNA polymerase iota in complex with T template DNA and incoming ddADP Deposited 2009-03-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 1–420（420 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；15% PEG 3350, 0.15 M CaCl2, 5% glycerol, 0.005M DTT, pH 7.5, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.253
3GV7 Human DNA polymerase iota in complex with T template DNA and incoming dTTP Deposited 2009-03-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa）	Not recorded	MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.5；15% PEG 5000MME, 0.2M NH4SO4, 0.1M MES 6.5, 5% glycerol, hanging drop	Resolution 2.20 Å R-free 0.258
3GV8 Human DNA polymerase iota in complex with T template DNA and incoming dGTP Deposited 2009-03-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa）	Not recorded	MG MAGNESIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6.5；15% PEG 5000MME, 0.2M NH4SO4, 0.1M MES 6.5, 5% glycerol, hanging drop	Resolution 2.00 Å R-free 0.248
3H40 Binary complex of human DNA polymerase iota with template U/T Deposited 2009-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–414（389 aa） Fragment：UNP residues 26-414, UmuC domain, DNA binding domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15 % PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.30 Å R-free 0.277
3H4B Ternary complex of human DNA polymerase iota with template U/T and incoming dATP Deposited 2009-04-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 25–414（390 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES , pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.281
3H4D Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP Deposited 2009-04-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 25–414（390 aa） Fragment：polymerase iota	Not recorded	MG MAGNESIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 5K MME, 0.2-0.4 M Ammonium sulfate, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.270
3NGD Structural Basis for Proficient Incorporation of dTTP Opposite O6-methylguanine by Human DNA Polymerase Iota Deposited 2010-06-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–420（420 aa） Fragment：Catalytic Fragment, 1-420	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M ammonium sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.284
3OSN Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase Iota Deposited 2010-09-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–420（420 aa） Fragment：Catalytic fragment, residues 1-420	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M Ammonium Sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.241
3Q8P Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanine Deposited 2011-01-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa） Fragment：UNP residues 1-420	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.95 Å R-free 0.257
3Q8Q Human DNA polymerase iota incorporating dATP opposite 8-oxo-guanine Deposited 2011-01-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa） Fragment：UNP residues 1-420	Not recorded	MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.03 Å R-free 0.253
3Q8R Human DNA polymerase iota incorporating dGTP opposite 8-oxo-guanine Deposited 2011-01-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa） Fragment：UNP residues 1-420	Not recorded	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.45 Å R-free 0.280
3Q8S Human DNA polymerase iota incorporating dTTP opposite 8-oxo-guanine Deposited 2011-01-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–420（420 aa） Fragment：UNP residues 1-420	Not recorded	MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.15M NH4SO4, 0.1M MES 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.09 Å R-free 0.266
4EBC Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota Deposited 2012-03-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	0OH North-methanocarba-2'-deoxyadenosine triphosphate × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.253
4EBE Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota Deposited 2012-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 10% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.265
4EYH Human DNA polymerase iota incorporating dCTP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion Deposited 2012-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.2 M MH4SO4, 0.1 M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.90 Å R-free 0.281
4EYI Human DNA polymerase iota incorporating dATP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion Deposited 2012-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15% PEG 5000MME, 0.2 M NH4SO4, 0.1M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.90 Å R-free 0.264
4FS1 Base pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota Deposited 2012-06-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa）	Not recorded	MG MAGNESIUM ION × 3 NA SODIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.9；277 K；210 microM polymerase iota, 253 microM DNA complex, 10 mM MgCl2, 20 mM dTTP; mix 1:1 ratio with precipitant, 0.1 M MES (pH 6.5), 0.3 M (NH4)2SO4, 17% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.270
4FS2 Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota Deposited 2012-06-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa）	Not recorded	MG MAGNESIUM ION × 3 NA SODIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.9；277 K；210 microM polymerase iota, 253 microM DNA complex, 10 mM MgCl2, 20 mM dTTP; mix 1:1 ratio with precipitant, 0.1 M MES (pH 6.5), 0.3 M (NH4)2SO4, 17% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.261
5KT2 Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；13% PEG MME 5000, 0.1M MES, 0.3M ammonium sulfate	Resolution 2.49 Å R-free 0.249
5KT3 Teranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa） Fragment：UNP residues 26-445	Not recorded	0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate	Resolution 2.64 Å R-free 0.248
5KT4 Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–445（445 aa） Fragment：UNP residues 1-445	Not recorded	0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate	Resolution 2.78 Å R-free 0.249
5KT5 Teranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–445（445 aa） Fragment：UNP residues 1-445	Not recorded	MN MANGANESE (II) ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate	Resolution 2.80 Å R-free 0.266
5KT6 Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mg2+ Deposited 2016-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–445（445 aa） Fragment：UNP residues 1-445	Not recorded	0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate	Resolution 3.54 Å R-free 0.244
5KT7 Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mn2+ Deposited 2016-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–445（445 aa）	Not recorded	MN MANGANESE (II) ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate	Resolution 3.15 Å R-free 0.236
5ULW Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine Deposited 2017-01-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa）	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；50 mM MES, pH 6.0, 18 % PEG 5KMME, 0.4 M Ammonium Sulfate	Resolution 2.62 Å R-free 0.248
5ULX Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dCTP Deposited 2017-01-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 26–445（420 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100 mM MES, pH 6.0, 14 % PEG 5KMME, 0.4 M Ammonium Sulfate	Resolution 1.96 Å R-free 0.239
9DDR Ternary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP Deposited 2024-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES pH 7 1.5-1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.15 Å R-free 0.280
9DQT Binary substrate complex of DNA polymerase iota with DNA (template A) Deposited 2024-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 3.19 Å R-free 0.364
9DQU Product complex of DNA polymerase iota with Pyrophosphate Deposited 2024-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	POP PYROPHOSPHATE 2- × 2 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.20 Å R-free 0.278
9DR7 Product complex of DNA polymerase iota with 2 monophosphates Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.45 Å R-free 0.312
9DR9 Binary product complex of DNA polymerase iota with DNA Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.21 Å R-free 0.297
9DRB Binary complex of DNA polymerase iota with product DNA Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.36 Å R-free 0.324
9DRC Ternary substrate complex of DNA polymerase iota R71A mutant with DNA (template A) and dTTP Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 - 1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.45 Å R-free 0.294
9NJH Translocated product complex of DNA polymerase iota with DNA (template A) Deposited 2025-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 26–445（420 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA	Resolution 2.29 Å R-free 0.288

52 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 26–445

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	4ebd
Deposition date deposition_date	2012-03-23
Structure title title	Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota
Keywords keywords	polymerase, 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	23.63 Å
Radius of gyration Rg (electron density) rg_electron	23.19 Å
Forward intensity I(0) i0	79913400.00
Molecular weight molecular_weight	44906.0 kDa
Excluded volume excluded_volume	42328 Å³
Envelope volume envelope_volume	71939 Å³
Hydration-shell volume shell_volume	25990 Å³
Envelope diameter envelope_diameter	87.2 Å
Shell Rg shell_rg	30.30 Å
Envelope Rg envelope_rg	23.40 Å
Shape Rg shape_rg	23.19 Å
Total Rg total_rg	23.78 Å
Total atoms total_atoms	3371
Residues n_residues	391
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	80.3 Å
Rg (real space) rg_real	23.58 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	7.9910e+07
I(0) uncertainty (real space) i0_real_error	1.2490e+06
Rg (reciprocal space) rg_reciprocal	23.60 Å
I(0) (reciprocal space) i0_reciprocal	79910000.0000
Solution quality estimate total_estimate	0.7946
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.216
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17040000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; 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 iota
Molecular weight formula_weight	47027.3 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	3517

MELADVGAAASSQGVHDQVLPTPNASSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYSSEKHYGRESRQCPIPSHVIQKLGTGNYDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLKALNTAK

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(PAPGPGPAPCPCP*(DOC))-3'
Molecular weight formula_weight	2091.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

AGGACCC

Entity 3 Entity 3 polymer

Description description	5'-D(PCPTPGPGPGPTPCPCP*T)-3'
Molecular weight formula_weight	2722.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CTGGGTCCT

Entity 4 Entity 4 non-polymer

Description description	;South-methanocarba-2'-deoxyadenosine triphosphate ;
Molecular weight formula_weight	501.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4ebda1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

Domain ID domain_id	d4ebda2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
Family Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

CATH v4.4 (4 domains)

Domain ID domain_id	4ebdA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4ebdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	4ebdA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	4ebdA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

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8. Citations (1)

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Unit-cell length a length_a	97.776 Å
Unit-cell length b length_b	97.776 Å
Unit-cell length c length_c	202.739 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.571 Å
Low-resolution limit resolution_low	48.888 Å
R factor r_factor	0.2120
R_work r_work	0.2062
R_free r_free	0.2629

fit	/app/data/saxs_computation/eb/4ebd/4ebd.fit
pddf	/app/data/pr_computation/eb/4ebd/4ebd.pr.out
profile	/app/data/saxs_computation/eb/4ebd/4ebd.dat

Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

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

DNA polymerase iota

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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)