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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P49642 New Search
23PDB entries
33Biological assembly
33chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method 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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric（23） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.