4P7I

Crystal structure of the Merlin FERM/DCAF1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1074/jbc.M114.551184

  • 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 chiefl ...

    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.,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, the Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China, and mzhang@ust.hk.,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, the Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China, and the Department of Biology, South University of Science and Technology of China, Shenzhen, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Merlin
A, B
317Mus musculusMutation(s): 0 
Gene Names: Nf2 (Nf-2)
Find proteins for P46662 (Mus musculus)
Go to UniProtKB:  P46662
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
C, D
67Homo sapiensMutation(s): 0 
Gene Names: DCAF1 (KIAA0800, RIP, VPRBP)
Find proteins for Q9Y4B6 (Homo sapiens)
Go to Gene View: DCAF1
Go to UniProtKB:  Q9Y4B6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.104α = 90.00
b = 97.104β = 90.00
c = 224.339γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
Blu-Icedata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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