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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.262 (Depositor), 0.264 (DCC)
R-Value Work:
0.219 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53135
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08032
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.262 (Depositor), 0.264 (DCC)
R-Value Work: 0.219 (Depositor), 0.220 (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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

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