4P7I

Crystal structure of the Merlin FERM/DCAF1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of the binding of Merlin FERM domain to the E3 ubiquitin ligase substrate adaptor DCAF1.

Li, Y.Wei, Z.Zhang, J.Yang, Z.Zhang, M.

(2014) J Biol Chem 289: 14674-14681

  • DOI: https://doi.org/10.1074/jbc.M114.551184
  • Primary Citation of Related Structures:  
    4P7I

  • PubMed Abstract: 

    The tumor suppressor gene Nf2 product, Merlin, plays vital roles in controlling proper development of organ sizes by specifically binding to a large number of target proteins localized both in cytoplasm and nuclei. The FERM domain of Merlin is chiefly responsible for its binding to target proteins, although the molecular basis governing these interactions are poorly understood due to lack of structural information. Here, we report the crystal structure of the Merlin FERM domain in complex with its binding domain derived from the E3 ubiquitin ligase substrate adaptor DCAF1 (also known as VPRBP). Unlike target binding modes found in ERM proteins, the Merlin-FERM binding domain of DCAF1 folds as a β-hairpin and binds to the α1/β5-groove of the F3 lobe of Merlin-FERM via extensive hydrophobic interactions. In addition to providing the first structural glimpse of a Merlin-FERM·target complex, the structure of the Merlin·DCAF1 complex is likely to be valuable for understanding the interactions of Merlin with its binding partners other than DCAF1.


  • Organizational Affiliation

    From the Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Merlin
A, B
317Mus musculusMutation(s): 0 
Gene Names: Nf2Nf-2
UniProt
Find proteins for P46662 (Mus musculus)
Explore P46662 
Go to UniProtKB:  P46662
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46662
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VPRBP
C, D
67Homo sapiensMutation(s): 0 
Gene Names: VPRBPDCAF1KIAA0800RIP
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens)
Explore Q9Y4B6 
Go to UniProtKB:  Q9Y4B6
PHAROS:  Q9Y4B6
GTEx:  ENSG00000145041 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4B6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.104α = 90
b = 97.104β = 90
c = 224.339γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RGC of Hong KongHong Kong663610, 663811, 663812, HKUST6/CRF/10, SEG_HKUST06, AoE/M09/12, and T13-607/12R

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Data collection
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description