5E4X

Crystal structure of cpSRP43 chromodomain 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.

Horn, A.Hennig, J.Ahmed, Y.L.Stier, G.Wild, K.Sattler, M.Sinning, I.

(2015) Nat Commun 6: 8875-8875

  • DOI: https://doi.org/10.1038/ncomms9875
  • Primary Citation of Related Structures:  
    2N88, 5E4W, 5E4X

  • PubMed Abstract: 

    Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 43 kDa protein, chloroplastic50Arabidopsis thalianaMutation(s): 0 
Gene Names: CAOCPSRP43At2g47450T30B22.25
UniProt
Find proteins for O22265 (Arabidopsis thaliana)
Explore O22265 
Go to UniProtKB:  O22265
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22265
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.86α = 90
b = 103.86β = 90
c = 103.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description