4lil

Crystal structure of the catalytic subunit of human primase bound to UTP and Mn

Method: X-RAY DIFFRACTION D_max: 81.2 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 1–408	Fragment：Catalytic subunit p48, UNP residues 1-390 (delta 360-379)	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

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 4LIL	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 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）	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 mutation/modification 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
4BPW Crystal structure of human primase bound to UTP Deposited 2013-05-28	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：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
4BPW Crystal structure of human primase bound to UTP Deposited 2013-05-28	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 C 1–420（420 aa） 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
4BPX Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha Deposited 2013-05-28	Different construct Different mutation/modification 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 mutation/modification 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 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
4MHQ Crystal structure of human primase catalytic subunit Deposited 2013-08-30	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） 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 32 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 5–392； UniProt 1–408

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	4lil
Deposition date deposition_date	2013-07-02
Structure title title	Crystal structure of the catalytic subunit of human primase bound to UTP and Mn
Keywords keywords	Prim fold, 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	24.43 Å
Radius of gyration Rg (electron density) rg_electron	23.60 Å
Forward intensity I(0) i0	32660100.00
Molecular weight molecular_weight	44498.0 kDa
Excluded volume excluded_volume	55855 Å³
Envelope volume envelope_volume	66179 Å³
Hydration-shell volume shell_volume	24159 Å³
Envelope diameter envelope_diameter	84.0 Å
Shell Rg shell_rg	29.99 Å
Envelope Rg envelope_rg	24.09 Å
Shape Rg shape_rg	23.63 Å
Total Rg total_rg	24.26 Å
Total atoms total_atoms	3129
Residues n_residues	370
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	81.2 Å
Rg (real space) rg_real	24.54 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.2660e+07
I(0) uncertainty (real space) i0_real_error	4.9480e+05
Rg (reciprocal space) rg_reciprocal	24.52 Å
I(0) (reciprocal space) i0_reciprocal	32660000.0000
Solution quality estimate total_estimate	0.8725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.272
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5945000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.975

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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	46471.2 kDa
EC 编号 ec_number	2.7.7.-
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	3171

GPGSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDATRDYKKTSLAPYVKVFEHFLENLDKSRKG

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;URIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	484.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4lilA00
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

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8. Citations (1)

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Unit-cell length a length_a	79.346 Å
Unit-cell length b length_b	79.346 Å
Unit-cell length c length_c	148.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	44.731 Å
R factor r_factor	0.2153
R_work r_work	0.2136
R_free r_free	0.2484

fit	/app/data/saxs_computation/li/4lil/4lil.fit
pddf	/app/data/pr_computation/li/4lil/4lil.pr.out
profile	/app/data/saxs_computation/li/4lil/4lil.dat