4bpw

Crystal structure of human primase bound to UTP

Method: X-RAY DIFFRACTION D_max: 138.5 Å Quality: GOOD

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

DNA PRIMASE SMALL 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 1–420	Fragment：PRIS Mutation：YES	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 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 3.00 Å R-free 0.253
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–420	Fragment：PRIS Mutation：YES	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 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 3.00 Å R-free 0.253

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 4BPW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa）	Mutation：YES	ZN ZINC ION × 1 GOL GLYCEROL × 4	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 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–420（420 aa）	Mutation：YES	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 2.70 Å R-free 0.245
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 C 1–420（420 aa）	Mutation：YES	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa）	Mutation：YES	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
4LIK Crystal structure of the catalytic subunit of human primase Deposited 2013-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–408（408 aa） Fragment：Catalytic subunit p48, UNP residues 1-390 (delta 360-379)	Not recorded	ZN ZINC ION × 1 CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；200 mM Sodium Citrate and 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.70 Å R-free 0.198
4LIL Crystal structure of the catalytic subunit of human primase bound to UTP and Mn Deposited 2013-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–408（408 aa） Fragment：Catalytic subunit p48, UNP residues 1-390 (delta 360-379)	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；0.2M K/Na Tartrate and 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.60 Å R-free 0.248
4MHQ Crystal structure of human primase catalytic subunit Deposited 2013-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–420（420 aa） Fragment：Full length	Not recorded	ZN ZINC ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；0.1M Na-acetate, 0.2M Tri-Na-citrate, 20% PEG3350, 0.1M Na-acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.233
4RR2 Crystal structure of human primase Deposited 2014-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–420（420 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–420（420 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
5EXR Crystal structure of human primosome Deposited 2015-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–420（420 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–420（420 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
6R4S Crystal structure of the Pri1 subunit of human primase bound to ATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.75 Å R-free 0.269
6R4S Crystal structure of the Pri1 subunit of human primase bound to ATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.75 Å R-free 0.269
6R4T Crystal structure of the Pri1 subunit of human primase bound to vidarabine triphosphate Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 1 HEJ 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.35 Å R-free 0.239
6R4T Crystal structure of the Pri1 subunit of human primase bound to vidarabine triphosphate Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 1 HEJ 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.35 Å R-free 0.239
6R4U Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 HFD 2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.20 Å R-free 0.223
6R4U Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 HFD 2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 2.20 Å R-free 0.223
6R5D Crystal structure of the Pri1 subunit of human primase bound to dATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 1.95 Å R-free 0.214
6R5D Crystal structure of the Pri1 subunit of human primase bound to dATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 1.95 Å R-free 0.214
6R5E Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 JSQ 2-fluoro-ATP × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 1.85 Å R-free 0.206
6R5E Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP Deposited 2019-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–407（407 aa）	Not recorded	ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 JSQ 2-fluoro-ATP × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate	Resolution 1.85 Å R-free 0.206
6RB4 Crystal structure of the Pri1 subunit of human primase Deposited 2019-04-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–407（407 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；100mM Bis Tris propane pH 6.5, 24 % PEG 3350, 150 mM NaF	Resolution 1.50 Å R-free 0.215
7OPL CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 Deposited 2021-06-01	Different construct Different mutation/modification 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 C 1–420（420 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 mutation/modification 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 A 1–420（420 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 mutation/modification 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 O 1–420（420 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 mutation/modification 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 D 2–420（419 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 mutation/modification 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 D 2–420（419 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
8D9D Human DNA polymerase-alpha/primase elongation complex II bound to primer/template Deposited 2022-06-09	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 × 4 PDB declaration: hexameric	Chain A 1–420（420 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 mutation/modification 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 C 1–420（420 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 mutation/modification 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 A 1–412（412 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 mutation/modification 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 A 1–412（412 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

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

View Construct and Data Evidence

UniProt name	PRI1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–423； UniProt 1–420 Author chain C； PDBConstruct 4–423； UniProt 1–420

DNA PRIMASE LARGE SUBUNIT

HOMO SAPIENS

UniProt P49643

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–253	Fragment：PRIL, RESIDUES 1-253	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–253	Fragment：PRIL, RESIDUES 1-253	No other associated polymer	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4BPW	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
3Q36 Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit Deposited 2010-12-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 266–457（192 aa） Fragment：4Fe-4S cluster domain (UNP residues 266-457)	Not recorded	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
3Q36 Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit Deposited 2010-12-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 266–457（192 aa） Fragment：4Fe-4S cluster domain (UNP residues 266-457)	Not recorded	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
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 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 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
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 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 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 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–253； UniProt 1–253 Author chain D； PDBConstruct 1–253； UniProt 1–253

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	4bpw
Deposition date deposition_date	2013-05-28
Structure title title	Crystal structure of human primase bound to UTP
Keywords keywords	TRANSFERASE, DNA-DEPENDENT RNA POLYMERASE, DNA REPLICATION; 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	41.93 Å
Radius of gyration Rg (electron density) rg_electron	41.58 Å
Forward intensity I(0) i0	280491000.00
Molecular weight molecular_weight	139640.0 kDa
Excluded volume excluded_volume	176120 Å³
Envelope volume envelope_volume	253030 Å³
Hydration-shell volume shell_volume	52128 Å³
Envelope diameter envelope_diameter	140.3 Å
Shell Rg shell_rg	45.73 Å
Envelope Rg envelope_rg	39.99 Å
Shape Rg shape_rg	41.57 Å
Total Rg total_rg	41.88 Å
Total atoms total_atoms	19712
Residues n_residues	1176
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	138.5 Å
Rg (real space) rg_real	41.99 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	2.8050e+08
I(0) uncertainty (real space) i0_real_error	5.3630e+06
Rg (reciprocal space) rg_reciprocal	41.93 Å
I(0) (reciprocal space) i0_reciprocal	280500000.0000
Solution quality estimate total_estimate	0.8900
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.4 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.651
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21500000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.913

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA PRIMASE SMALL SUBUNIT
Molecular weight formula_weight	50108.0 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	19731

GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQAANPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLKKSDLQKDF

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	DNA PRIMASE LARGE SUBUNIT
Molecular weight formula_weight	29782.2 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	B,D

MEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLGVSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAVQSDERLQPLLNHL

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 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4bpwA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily	10 — DNA primase, PRIM domain

Domain ID domain_id	4bpwB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	4bpwC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily	10 — DNA primase, PRIM domain

Domain ID domain_id	4bpwD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Unit-cell length a length_a	116.394 Å
Unit-cell length b length_b	69.438 Å
Unit-cell length c length_c	127.087 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.003 Å
Low-resolution limit resolution_low	46.784 Å
R factor r_factor	0.2172
R_work r_work	0.2152
R_free r_free	0.2534

fit	/app/data/saxs_computation/bp/4bpw/4bpw.fit
pddf	/app/data/pr_computation/bp/4bpw/4bpw.pr.out
profile	/app/data/saxs_computation/bp/4bpw/4bpw.dat

Crystal structure of human primase bound to UTP

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

DNA PRIMASE SMALL SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

DNA PRIMASE LARGE SUBUNIT

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 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)