8j09

Crystal structure of the Sld3 Cdc45-binding-domain, in complex with Cdc45

Method: X-RAY DIFFRACTION D_max: 103.0 Å Quality: GOOD

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

DNA replication regulator SLD3

Saccharomyces cerevisiae S288C

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 154–420	Not recorded	Cell division control protein 45 × 1 （Q08032）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M sodium acetate, 0.1M Bis-Tris propane (pH6.5: pH8.5 = 3:7), 20%(w/v) PEG33500	Resolution 2.61 Å R-free 0.262

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 8J09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WI3 Crystal Structure of the Sld3/Treslin domain from yeast Sld3 Deposited 2013-09-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–430（283 aa） Fragment：UNP RESIDUES 148-430	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262
3WI3 Crystal Structure of the Sld3/Treslin domain from yeast Sld3 Deposited 2013-09-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 148–430（283 aa） Fragment：UNP RESIDUES 148-430	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262
3WI3 Crystal Structure of the Sld3/Treslin domain from yeast Sld3 Deposited 2013-09-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 148–430（283 aa） Fragment：UNP RESIDUES 148-430	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.262
9RHI pre-Initiation Complex on ARS1 DNA (monomer) Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain Q 1–668（668 aa） Chain T 1–668（668 aa）	Not recorded	ZN ZINC ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RHJ Pre-Initiation Complex on ARS1 DNA (dimer) Deposited 2025-06-09	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 × 30 PDB declaration: 32-meric	Chain Q 1–668（668 aa） Chain T 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9RHL Phospho-DH bound by Sld3-MBD on ARS1 DNA Deposited 2025-06-09	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 × 14 PDB declaration: 16-meric	Chain H 1–668（668 aa） Chain I 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9RHM Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain H 1–668（668 aa） Chain I 1–668（668 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLD3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 154–420

Cell division control protein 45

Saccharomyces cerevisiae S288C

UniProt Q08032

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–650	Not recorded	DNA replication regulator SLD3 × 1 （P53135）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M sodium acetate, 0.1M Bis-Tris propane (pH6.5: pH8.5 = 3:7), 20%(w/v) PEG33500	Resolution 2.61 Å R-free 0.262

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8J09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
28VY sCMGE assembled on ARS1 DNA with Sld2 and RPA Deposited 2026-02-23	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 × 13 PDB declaration: 15-meric	Chain E 1–197（197 aa） Chain E 204–650（447 aa）	Not recorded	MG MAGNESIUM ION × 6 ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
3JC5 Structure of the eukaryotic replicative CMG helicase and pumpjack motion Deposited 2015-11-24	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain c 1–650（650 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA；pH 7.5；20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA cryo-EM vitrification conditions Blot for 3 seconds before plunging；Cryogen ETHANE；Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 4.70 Å
3JC6 Structure of the eukaryotic replicative CMG helicase and pumpjack motion Deposited 2015-11-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 1–650（650 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA；pH 7.5；20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA cryo-EM vitrification conditions Blot for 3 seconds before plunging；Cryogen ETHANE；Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 3.70 Å R-free 0.331
3JC7 Structure of the eukaryotic replicative CMG helicase and pumpjack motion Deposited 2015-11-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain c 1–650（650 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA；pH 7.5；20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA cryo-EM vitrification conditions Blot for 3 seconds before plunging；Cryogen ETHANE；Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 4.80 Å
5U8S Structure of eukaryotic CMG helicase at a replication fork Deposited 2016-12-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å R-free 0.391
5U8T Structure of Eukaryotic CMG Helicase at a Replication Fork and Implications Deposited 2016-12-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain E 1–650（650 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å R-free 0.394
6HV9 S. cerevisiae CMG-Pol epsilon-DNA Deposited 2018-10-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain G 1–650（650 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.98 Å
6PTJ Structure of Ctf4 trimer in complex with one CMG helicase Deposited 2019-07-15	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain c 1–650（650 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6PTN Structure of Ctf4 trimer in complex with two CMG helicases Deposited 2019-07-16	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 × 25 PDB declaration: 25-meric	Chain H 1–650（650 aa） Chain h 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
6PTO Structure of Ctf4 trimer in complex with three CMG helicases Deposited 2019-07-16	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 × 36 PDB declaration: 36-meric	Chain E 1–650（650 aa） Chain e 1–650（650 aa） Chain r 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6SKL Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1 Deposited 2019-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain E 1–650（650 aa） Fragment：Mcm4	Not recorded	ZN ZINC ION × 5 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Three microlitres of sample was applied on a grid and incubated for 15-30 s at 4 degC before manually blotting with filter paper for 10 s and plunge-freezing in liquid ethane.	Resolution 3.70 Å
6U0M Structure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA Deposited 2019-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain E 5–650（646 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7PMK S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I) Deposited 2021-09-02	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 × 20 PDB declaration: 22-meric	Chain E 1–197（197 aa） Chain E 203–650（448 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
7PMN S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Deposited 2021-09-02	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 × 20 PDB declaration: 22-meric	Chain E 1–197（197 aa） Chain E 203–650（448 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
7QHS S. cerevisiae CMGE nucleating origin DNA melting Deposited 2021-12-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7Z13 S. cerevisiae CMGE dimer nucleating origin DNA melting Deposited 2022-02-24	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 × 26 PDB declaration: 28-meric	Chain E 1–198（198 aa） Chain E 203–650（448 aa） Chain L 1–198（198 aa） Chain L 203–650（448 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8 ZN ZINC ION × 14 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. 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 G 1–198（198 aa） Chain G 203–650（448 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. 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 G 1–198（198 aa） Chain G 203–650（448 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9C S. cerevisiae pol alpha - replisome complex 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 × 18 PDB declaration: eicosameric	Chain G 1–198（198 aa） Chain G 203–650（448 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8KG6 Yeast replisome in state I Deposited 2023-08-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric	Chain E 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 3.07 Å
8KG8 Yeast replisome in state II Deposited 2023-08-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain E 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.23 Å
8KG9 Yeast replisome in state III Deposited 2023-08-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain E 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.52 Å
8P5E S. cerevisiae nexus-sCMGE after DNA replication initiation Deposited 2023-05-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8P62 S. cerevisiae ssDNA-sCMGE after DNA replication initiation Deposited 2023-05-25	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8P63 S. cerevisiae consensus-sCMGE on ssDNA after DNA replication initiation Deposited 2023-05-25	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8W7M Yeast replisome in state V Deposited 2023-08-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain E 1–650（650 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.12 Å
8W7S Yeast replisome in state IV Deposited 2023-08-31	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain E 1–650（650 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 7.39 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain E 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9E2W Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 1 Deposited 2024-10-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain E 1–650（650 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 30 seconds after sample application; blot time 30 seconds with blot force 0	Resolution 3.30 Å
9E2X Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 2 Deposited 2024-10-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain E 1–650（650 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ZN ZINC ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 30 seconds after sample application; blot time 30 seconds with blot force 0	Resolution 3.50 Å
9E2Y Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 3 Deposited 2024-10-23	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain E 1–650（650 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Wait time 30 seconds after sample application; blot time 30 seconds with blot force 0	Resolution 3.20 Å
9RHI pre-Initiation Complex on ARS1 DNA (monomer) Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain E 1–197（197 aa） Chain E 204–650（447 aa）	Not recorded	ZN ZINC ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RHJ Pre-Initiation Complex on ARS1 DNA (dimer) Deposited 2025-06-09	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 × 30 PDB declaration: 32-meric	Chain E 1–197（197 aa） Chain E 204–650（447 aa） Chain L 1–197（197 aa） Chain L 204–650（447 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9RHM Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA Deposited 2025-06-09	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 × 17 PDB declaration: 19-meric	Chain E 1–197（197 aa） Chain E 204–650（447 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

34 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDC45_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–650； UniProt 1–650

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	8j09
Deposition date deposition_date	2023-04-10
Structure title title	Crystal structure of the Sld3 Cdc45-binding-domain, in complex with Cdc45
Keywords keywords	REPLICATION, DNA replication, CMG formation, Cdc45 recruitment, Sld3; REPLICATION
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	31.43 Å
Radius of gyration Rg (electron density) rg_electron	30.64 Å
Forward intensity I(0) i0	123782000.00
Molecular weight molecular_weight	91782.0 kDa
Excluded volume excluded_volume	116420 Å³
Envelope volume envelope_volume	144610 Å³
Hydration-shell volume shell_volume	39801 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	37.38 Å
Envelope Rg envelope_rg	30.72 Å
Shape Rg shape_rg	30.64 Å
Total Rg total_rg	31.25 Å
Total atoms total_atoms	6476
Residues n_residues	796
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	103.0 Å
Rg (real space) rg_real	31.44 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.2380e+08
I(0) uncertainty (real space) i0_real_error	2.0070e+06
Rg (reciprocal space) rg_reciprocal	31.44 Å
I(0) (reciprocal space) i0_reciprocal	123800000.0000
Solution quality estimate total_estimate	0.8925
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.0 Å
Skewness Skewness skewness	0.359
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40750000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA replication regulator SLD3
Molecular weight formula_weight	31118.2 kDa
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	6516

YSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSKKKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKGP

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cell division control protein 45
Molecular weight formula_weight	74324.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MYYGISQFSEAYNKILRNSSSHSSCQLVIFVSCLNIDALCATKMLSLLFKKQLVQSQIVPIFGYSELRRHYSQLDDNINSLLLVGFGGVIDLEAFLEIDPQEYVIDTDEKSGEQSFRRDIYVLDAHRPWNLDNIFGSQIIQCFDDGTVDDTLGEQKEAYYKLLELDEESGDDELSGDENDNNGGDDEATDADEVTDEDEEDEDETISNKRGNSSIGPNDLSKRKQRKKQIHEYEGVLEEYYSQGTTVVNSISAQIYSLLSAIGETNLSNLWLNILGTTSLDIAYAQVYNRLYPLLQDEVKRLTPSSRNSVKTPDTLTLNIQPDYYLFLLRHSSLYDSFYYSNYVNAKLSLWNENGKKRLHKMFARMGIPLSTAQETWLYMDHSIKRELGIIFDKNLDRYGLQDIIRDGFVRTLGYRGSISASEFVEALTALLEVGNSTDKDSVKINNDNNDDTDGEEEEDNSAQKLTNLRKRWVSNFWLSWDALDDRKVELLNRGIQLAQDLQRAIFNTGVAILEKKLIKHLRIYRLCVLQDGPDLDLYRNPLTLLRLGNWLIECCAESEDKQLLPMVLASIDENTDTYLVAGLTPRYPRGLDTIHTKKPILNNFSMAFQQITAETDAKVRIDNFESSIIEIRREDLSPFLEKLTLSGLL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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8. Citations (1)

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Unit-cell length a length_a	70.771 Å
Unit-cell length b length_b	107.569 Å
Unit-cell length c length_c	128.283 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	43.470 Å
R factor r_factor	0.2212
R_work r_work	0.2189
R_free r_free	0.2624

fit	/app/data/saxs_computation/j0/8j09/8j09.fit
pddf	/app/data/pr_computation/j0/8j09/8j09.pr.out
profile	/app/data/saxs_computation/j0/8j09/8j09.dat

Crystal structure of the Sld3 Cdc45-binding-domain, in complex with Cdc45

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

DNA replication regulator SLD3

State in the Current Structure

Other States of the Same Protein in the Database

Cell division control protein 45

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)