8IR2

Crystal structure of the SLF1 BRCT domain in complex with a Rad18 peptide containing pS442 and pS444


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into Rad18 targeting by the SLF1 BRCT domains.

Huang, W.Qiu, F.Zheng, L.Shi, M.Shen, M.Zhao, X.Xiang, S.

(2023) J Biol Chem 299: 105288-105288

  • DOI: https://doi.org/10.1016/j.jbc.2023.105288
  • Primary Citation of Related Structures:  
    8IR2, 8IR4

  • PubMed Abstract: 

    Rad18 interacts with the SMC5/6 localization factor 1 (SLF1) to recruit the SMC5/6 complex to DNA damage sites for repair. The mechanism of the specific Rad18 recognition by SLF1 is unclear. Here, we present the crystal structure of the tandem BRCT repeat (tBRCT) in SLF1 (SLF1 tBRCT ) bound with the interacting Rad18 peptide. Our structure and biochemical studies demonstrate that SLF1 tBRCT interacts with two phosphoserines and adjacent residues in Rad18 for high-affinity and specificity Rad18 recognition. We found that SLF1 tBRCT utilizes mechanisms common among tBRCTs as well as unique ones for Rad18 binding, the latter include interactions with an α-helical structure in Rad18 that has not been observed in other tBRCT-bound ligand proteins. Our work provides structural insights into Rad18 targeting by SLF1 and expands the understanding of BRCT-mediated complex assembly.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, P. R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SMC5-SMC6 complex localization factor protein 1
A, B
207Homo sapiensMutation(s): 0 
Gene Names: SLF1ANKRD32BRCTD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQI6 (Homo sapiens)
Explore Q9BQI6 
Go to UniProtKB:  Q9BQI6
PHAROS:  Q9BQI6
GTEx:  ENSG00000133302 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQI6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SER-ASP-SER-CYS-ASN-SER-SEP-SER-SEP-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
C, D
17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS91 (Homo sapiens)
Explore Q9NS91 
Go to UniProtKB:  Q9NS91
PHAROS:  Q9NS91
GTEx:  ENSG00000070950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NS91
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.352α = 90
b = 76.203β = 90
c = 141.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071205
National Natural Science Foundation of China (NSFC)China31870769

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release