3WI3 | pdb_00003wi3

Crystal Structure of the Sld3/Treslin domain from yeast Sld3

• PDB DOI: https://doi.org/10.2210/pdb3WI3/pdb

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


• Deposited: 2013-09-05 Released: 2014-08-20 
• Deposition Author(s): Itou, H., Araki, H., Shirakihara, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of the homology domain of the eukaryotic DNA replication proteins sld3/treslin.

Itou, H., Muramatsu, S., Shirakihara, Y., Araki, H.

(2014) Structure 22: 1341-1347

• PubMed: 25126958 
• DOI: https://doi.org/10.1016/j.str.2014.07.001
• Primary Citation Related Structures: 
  3WI3


• PubMed Abstract: 
  

  The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomal DNA. Yeast Sld3 and its metazoan counterpart Treslin are the hub proteins mediating protein associations critical for the helicase formation. Here, we show the crystal structure of the central domain of Sld3 that is conserved in Sld3/Treslin family of proteins. The domain consists of two segments with 12 helices and is sufficient to bind to Cdc45, the essential helicase component. The structure model of the Sld3-Cdc45 complex, which is crucial for the formation of the active helicase, is proposed.

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Organizational Affiliation: 
• Structural Biology Center, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan. Electronic address: [e-mail].
Division of Microbial Genetics, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan.
Structural Biology Center, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan.
Division of Microbial Genetics, National Institute of Genetics, Yata1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata1111, Mishima, Shizuoka 411-8540, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.51 kDa 
• Atom Count: 5,473 
• Modeled Residue Count: 632 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication regulator SLD3	A, B, C	292	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SLD3, YGL113W, G2980
UniProt
Find proteins for P53135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53135  Go to UniProtKB:  P53135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], DA [auth C], U [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth B], BA [auth B], CA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.264	α = 90
b = 92.82	β = 90
c = 160.87	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Itou, H., Araki, H., Shirakihara, Y.

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description