3WA0

Crystal structure of merlin complexed with DCAF1/VprBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of DDB1-and-Cullin 4-associated Factor 1 (DCAF1) recognition by merlin/NF2 and its implication in tumorigenesis by CD44-mediated inhibition of merlin suppression of DCAF1 function

Mori, T.Gotoh, S.Shirakawa, M.Hakoshima, T.

(2014) Genes Cells --: --

  • DOI: 10.1111/gtc.12161

  • PubMed Abstract: 
  • Merlin, a tumor suppressor encoded by the neurofibromatosis type 2 gene, has been shown to suppress tumorigenesis by inhibiting the Cullin 4-RING E3 ubiquitin ligase CRL4(DCAF) (1) in the nucleus. This inhibition is mediated by direct binding of merl ...

    Merlin, a tumor suppressor encoded by the neurofibromatosis type 2 gene, has been shown to suppress tumorigenesis by inhibiting the Cullin 4-RING E3 ubiquitin ligase CRL4(DCAF) (1) in the nucleus. This inhibition is mediated by direct binding of merlin to DDB1-and-Cullin 4-associated Factor 1 (DCAF1), yet the binding mode of merlin to DCAF1 is not well defined. Here, we report structural and biophysical studies of the merlin binding to DCAF1 and its interference with CD44 binding. The crystal structure of the merlin FERM domain bound to the DCAF1 C-terminal acidic tail reveals that the hydrophobic IILXLN motif located at the C-terminal end of DCAF1 binds subdomain C of the FERM domain by forming a β-strand. The binding site and mode resemble that of merlin binding to the CD44 cytoplasmic tail. Competition binding assay showed that CD44 and DCAF1 compete for binding to the merlin FERM domain in solution. The CD44 cytoplasmic tail is known to be cleaved for nuclear translocation by regulated intra-membrane proteolysis (RIP). Our structure implies that, in the nucleus, the CD44 cytoplasmic tail cleaved by RIP could release DCAF1 from merlin by competing for binding to the merlin FERM domain, which results in the inhibition of merlin-mediated suppression of tumorigenesis.


    Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Merlin
A, B, C, D, E, F
301Mus 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
G, H
96Homo sapiensMutation(s): 0 
Gene Names: DCAF1 (KIAA0800, RIP, VPRBP)
Find proteins for Q9Y4B6 (Homo sapiens)
Go to Gene View: DCAF1
Go to UniProtKB:  Q9Y4B6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
J
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Protein VPRBP
K
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
I, J, K
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.363α = 90.00
b = 135.760β = 90.00
c = 238.495γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references, Structure summary