6TYD

Structure of human LDB1 in complex with SSBP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human LDB1 in complex with SSBP2.

Wang, H.Kim, J.Wang, Z.Yan, X.X.Dean, A.Xu, W.

(2020) Proc.Natl.Acad.Sci.USA 117: 1042-1048

  • DOI: 10.1073/pnas.1914181117

  • PubMed Abstract: 
  • The Lim domain binding proteins (LDB1 and LDB2 in human and Chip in <i>Drosophila </i>) play critical roles in cell fate decisions through partnership with multiple Lim-homeobox and Lim-only proteins in diverse developmental systems including cardio ...

    The Lim domain binding proteins (LDB1 and LDB2 in human and Chip in Drosophila ) play critical roles in cell fate decisions through partnership with multiple Lim-homeobox and Lim-only proteins in diverse developmental systems including cardiogenesis, neurogenesis, and hematopoiesis. In mammalian erythroid cells, LDB1 dimerization supports long-range connections between enhancers and genes involved in erythropoiesis, including the β-globin genes. Single-stranded DNA binding proteins (SSBPs) interact specifically with the LDB/Chip conserved domain (LCCD) of LDB proteins and stabilize LDBs by preventing their proteasomal degradation, thus promoting their functions in gene regulation. The structural basis for LDB1 self-interaction and interface with SSBPs is unclear. Here we report a crystal structure of the human LDB1/SSBP2 complex at 2.8-Å resolution. The LDB1 dimerization domain (DD) contains an N-terminal nuclear transport factor 2 (NTF2)-like subdomain and a small helix 4-helix 5 subdomain, which together form the LDB1 dimerization interface. The 2 LCCDs in the symmetric LDB1 dimer flank the core DDs, with each LCCD forming extensive interactions with an SSBP2 dimer. The conserved linker between LDB1 DD and LCCD covers a potential ligand-binding pocket of the LDB1 NTF2-like subdomain and may serve as a regulatory site for LDB1 structure and function. Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.


    Organizational Affiliation

    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.,National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China.,Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98195.,National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; xuwq2@shanghaitech.edu.cn snow@ibp.ac.cn ann.dean@nih.gov.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 xuwq2@shanghaitech.edu.cn snow@ibp.ac.cn ann.dean@nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIM domain-binding protein 1
V
231Homo sapiensMutation(s): 0 
Gene Names: LDB1 (CLIM2)
Find proteins for Q86U70 (Homo sapiens)
Go to Gene View: LDB1
Go to UniProtKB:  Q86U70
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein 2
A, B
95Homo sapiensMutation(s): 0 
Gene Names: SSBP2 (SSDP2)
Find proteins for P81877 (Homo sapiens)
Go to Gene View: SSBP2
Go to UniProtKB:  P81877
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
V
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.322α = 90.00
b = 104.322β = 90.00
c = 250.419γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Database references
  • Version 1.2: 2020-01-29
    Type: Database references