3q36

Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit

Method: X-RAY DIFFRACTION D_max: 99.2 Å Quality: REASONABLE

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

DNA primase large subunit

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 266–457	Fragment：4Fe-4S cluster domain (UNP residues 266-457)	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate, 15% w/v PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.50 Å R-free 0.250
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 266–457	Fragment：4Fe-4S cluster domain (UNP residues 266-457)	SF4 IRON/SULFUR CLUSTER × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate, 15% w/v PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.50 Å R-free 0.250

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 3Q36	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3L9Q Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain Deposited 2010-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 272–464（193 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-464) Chain B 272–464（193 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-464)	Not recorded	SF4 IRON/SULFUR CLUSTER × 4 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；0.1 M Tris pH 8.5, 15% PEG 3250, 0.2 M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.169
3L9Q Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain Deposited 2010-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 272–464（193 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-464) Chain B 272–464（193 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-464)	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；0.1 M Tris pH 8.5, 15% PEG 3250, 0.2 M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.169
4BPU Crystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain. Deposited 2013-05-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–253（253 aa） Fragment：RESIDUES 1-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL	Resolution 2.70 Å R-free 0.245
4BPU Crystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain. Deposited 2013-05-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–253（253 aa） Fragment：RESIDUES 1-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL	Resolution 2.70 Å R-free 0.245
4BPW Crystal structure of human primase bound to UTP Deposited 2013-05-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–253（253 aa） Fragment：PRIL, RESIDUES 1-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL AND 1,3-PROPANEDIOL.	Resolution 3.00 Å R-free 0.253
4BPW Crystal structure of human primase bound to UTP Deposited 2013-05-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–253（253 aa） Fragment：PRIL, RESIDUES 1-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL AND 1,3-PROPANEDIOL.	Resolution 3.00 Å R-free 0.253
4BPX Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha Deposited 2013-05-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 19–253（235 aa） Fragment：PRIMASE-BINDING MOTIF RESIDUES 1445-1462, PRIL RESIDUES 19-253	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL.	Resolution 3.40 Å R-free 0.267
4BPX Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha Deposited 2013-05-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–253（235 aa） Fragment：PRIMASE-BINDING MOTIF RESIDUES 1445-1462, PRIL RESIDUES 19-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL.	Resolution 3.40 Å R-free 0.267
4RR2 Crystal structure of human primase Deposited 2014-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–509（509 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；50 mM Tris-HCl pH 8.5, 7.5% v/v ethanol and 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.65 Å R-free 0.271
4RR2 Crystal structure of human primase Deposited 2014-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–509（509 aa）	Not recorded	ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；50 mM Tris-HCl pH 8.5, 7.5% v/v ethanol and 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.65 Å R-free 0.271
5DQO Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain Deposited 2015-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 272–464（193 aa） Fragment：p58C domain (UNP residues 272-464) Chain B 272–464（193 aa） Fragment：p58C domain (UNP residues 272-464)	Mutation：Y347F Mutation：Y347F	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；300 mM lithium sulfate, 100 mM Tris, pH 8.5, 20% PEG3350	Resolution 2.30 Å R-free 0.275
5DQO Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain Deposited 2015-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 272–464（193 aa） Fragment：p58C domain (UNP residues 272-464) Chain D 272–464（193 aa） Fragment：p58C domain (UNP residues 272-464)	Mutation：Y347F Mutation：Y347F	SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；300 mM lithium sulfate, 100 mM Tris, pH 8.5, 20% PEG3350	Resolution 2.30 Å R-free 0.275
5EXR Crystal structure of human primosome Deposited 2015-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–509（509 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA	Resolution 3.60 Å R-free 0.326
5EXR Crystal structure of human primosome Deposited 2015-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–509（509 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA	Resolution 3.60 Å R-free 0.326
5F0Q Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer Deposited 2015-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain A 266–456（191 aa） Fragment：UNP residues 266-456	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride	Resolution 2.21 Å R-free 0.258
5F0Q Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer Deposited 2015-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain B 266–456（191 aa） Fragment：UNP residues 266-456	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride	Resolution 2.21 Å R-free 0.258
5F0S Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion Deposited 2015-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain A 266–456（191 aa） Fragment：UNP residues 266-456	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Reservoir solution containe 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride. To exchange Mg to Mn crystals were soaked for 5 min in a reservoir solution containing 2 mM manganese chloride instead of magnesium chloride.	Resolution 3.00 Å R-free 0.269
5F0S Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion Deposited 2015-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain B 266–456（191 aa） Fragment：UNP residues 266-456	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Reservoir solution containe 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride. To exchange Mg to Mn crystals were soaked for 5 min in a reservoir solution containing 2 mM manganese chloride instead of magnesium chloride.	Resolution 3.00 Å R-free 0.269
5I7M Crystal structure of Y345F mutant of human primase p58 iron-sulfur cluster domain Deposited 2016-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 272–457（186 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-457) Chain B 272–457（186 aa） Fragment：iron-sulfur cluster domain (UNP residues 272-457)	Mutation：Y345F Mutation：Y345F	SF4 IRON/SULFUR CLUSTER × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；75 mg/mL p58C Y345F in 20 mM MES, pH 6.5, 50 mM sodium chloride, reservoir solution: 100 mM Tris, pH 8.5, 150 mM lithium sulfate, 18% PEG3350	Resolution 1.93 Å R-free 0.250
6DHW Crystal structure of primase iron-sulfur domain (266-457) Deposited 2018-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 266–457（192 aa） Chain B 266–457（192 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；100 mM TRIS-HCl pH 8.5, 400 mM LiSO4, 18% PEG3350	Resolution 2.01 Å R-free 0.211
6DHW Crystal structure of primase iron-sulfur domain (266-457) Deposited 2018-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 266–457（192 aa） Chain B 266–457（192 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；100 mM TRIS-HCl pH 8.5, 400 mM LiSO4, 18% PEG3350	Resolution 2.01 Å R-free 0.211
7OPL CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 Deposited 2021-06-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–509（509 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
7U5C Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state Deposited 2022-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain B 1–509（509 aa）	Not recorded	ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8B9D Human replisome bound by Pol Alpha Deposited 2022-10-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain P 1–509（509 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8D0B Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template Deposited 2022-05-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain E 16–256（241 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8D0K Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC Deposited 2022-05-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain E 2–509（508 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
8D96 Human DNA polymerase alpha/primase elongation complex I bound to primer/template Deposited 2022-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 1–509（509 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
8D9D Human DNA polymerase-alpha/primase elongation complex II bound to primer/template Deposited 2022-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–509（509 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
8QJ7 Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1 Deposited 2023-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–509（509 aa）	Not recorded	ZN ZINC ION × 3 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8VY3 Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio) Deposited 2024-02-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 22–455（434 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
9C8V Human DNA polymerase alpha/primase - CHAPSO (4 mM) Deposited 2024-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 22–455（434 aa）	Not recorded	ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å

21 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRI2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–192； UniProt 266–457 Author chain B； PDBConstruct 1–192； UniProt 266–457

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	3q36
Deposition date deposition_date	2010-12-21
Structure title title	Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit
Keywords keywords	;pol alpha, primase, DNA replication, polymerase, iron-sulfur cluster, DNA-binding, dna-directed RNA polymerase, metal-binding, nucleotidyltransferase, phosphoprotein, primosome, transcription, TRANSFERASE ;; TRANSFERASE
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	27.25 Å
Radius of gyration Rg (electron density) rg_electron	27.30 Å
Forward intensity I(0) i0	30109500.00
Molecular weight molecular_weight	42008.0 kDa
Excluded volume excluded_volume	52209 Å³
Envelope volume envelope_volume	64191 Å³
Hydration-shell volume shell_volume	21026 Å³
Envelope diameter envelope_diameter	102.5 Å
Shell Rg shell_rg	32.15 Å
Envelope Rg envelope_rg	27.54 Å
Shape Rg shape_rg	27.41 Å
Total Rg total_rg	27.50 Å
Total atoms total_atoms	2923
Residues n_residues	356
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	99.2 Å
Rg (real space) rg_real	27.64 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	3.0110e+07
I(0) uncertainty (real space) i0_real_error	5.4580e+05
Rg (reciprocal space) rg_reciprocal	27.52 Å
I(0) (reciprocal space) i0_reciprocal	30110000.0000
Solution quality estimate total_estimate	0.7440
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.573
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14570000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.445; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.387; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA primase large subunit
Molecular weight formula_weight	22084.3 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2944

GNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG

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 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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8. Citations (1)

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Unit-cell length a length_a	126.476 Å
Unit-cell length b length_b	83.724 Å
Unit-cell length c length_c	47.561 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	31.160 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2500

fit	/app/data/saxs_computation/q3/3q36/3q36.fit
pddf	/app/data/pr_computation/q3/3q36/3q36.pr.out
profile	/app/data/saxs_computation/q3/3q36/3q36.dat