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6r5e

Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP

Method: X-RAY DIFFRACTION Dmax: 108.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA primase small subunit

Homo sapiens

UniProt P49642

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 1–407 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 1–407 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

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 6R5E 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 construct 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
6RB4 Crystal structure of the Pri1 subunit of human primase Deposited 2019-04-09 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 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 4–410； UniProt 1–407 Author chain E； PDBConstruct 4–410； UniProt 1–407

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

SAXS profile for 6r5e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6r5e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6r5e
Deposition date deposition_date2019-03-24
Structure title titleCrystal structure of the Pri1 subunit of human primase bound to 2F-ATP
Keywords keywordsPrimase, DNA-dependent RNA polymerase, ATP, priming, replication; REPLICATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.95 Å
Radius of gyration Rg (electron density) rg_electron31.25 Å
Forward intensity I(0) i0134003000.00
Molecular weight molecular_weight92967.0 kDa
Excluded volume excluded_volume116630 ų
Envelope volume envelope_volume144760 ų
Hydration-shell volume shell_volume38535 ų
Envelope diameter envelope_diameter115.1 Å
Shell Rg shell_rg38.15 Å
Envelope Rg envelope_rg31.45 Å
Shape Rg shape_rg31.26 Å
Total Rg total_rg31.78 Å
Total atoms total_atoms12992
Residues n_residues765
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.8 Å
Rg (real space) rg_real31.92 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real1.3400e+08
I(0) uncertainty (real space) i0_real_error2.2680e+06
Rg (reciprocal space) rg_reciprocal31.94 Å
I(0) (reciprocal space) i0_reciprocal134000000.0000
Solution quality estimate total_estimate0.8802
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.6 Å
Skewness Skewness skewness0.274
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57350000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.926
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6r5eA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily10 — DNA primase, PRIM domain
Domain ID domain_id6r5eE00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily10 — DNA primase, PRIM domain
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8. Citations (1)

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9. Files and Curves (10)