8J09 | pdb_00008j09

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

• PDB DOI: https://doi.org/10.2210/pdb8J09/pdb

• Classification: REPLICATION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-10 Released: 2024-05-29 
• Deposition Author(s): Li, H., Ishizaka, I., Kato, K., Sun, X., Muramatsu, S., Itou, H., Ose, T., Araki, H., Yao, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Models: experimental

Literature

Structural and functional insights into Cdc45 recruitment by Sld7-Sld3 for CMG complex formation

Li, H., Ishizaki, I., Kato, K., Sun, X., Muramatsu, S., Itou, H., Ose, T., Araki, H., Yao, M.

(2024) Elife 

• DOI: https://doi.org/10.7554/elife.101717.1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.44 kDa 
• Atom Count: 6,516 
• Modeled Residue Count: 796 
• Deposited Residue Count: 917 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication regulator SLD3	A	267	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SLD3
UniProt
Find proteins for P53135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53135  Go to UniProtKB:  P53135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 45	B	650	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CDC45
UniProt
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08032  Go to UniProtKB:  Q08032

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.771	α = 90
b = 107.569	β = 90
c = 128.283	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Li, H., Ishizaka, I., Kato, K., Sun, X., Muramatsu, S., Itou, H., Ose, T., Araki, H., Yao, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H01754
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101071
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101083

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Database references, Structure summary
• Version 1.2: 2024-11-27
  Changes: Structure summary