4LG6 | pdb_00004lg6

Crystal structure of ANKRA2-CCDC8 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.208 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4LG6

This is version 1.3 of the entry. See complete history

Literature

Ankyrin Repeats of ANKRA2 Recognize a PxLPxL Motif on the 3M Syndrome Protein CCDC8.

Nie, J.Xu, C.Jin, J.Aka, J.A.Tempel, W.Nguyen, V.You, L.Weist, R.Min, J.Pawson, T.Yang, X.J.

(2015) Structure 23: 700-712

  • DOI: https://doi.org/10.1016/j.str.2015.02.001
  • Primary Citation Related Structures: 
    4LG6

  • PubMed Abstract: 

    Peptide motifs are often used for protein-protein interactions. We have recently demonstrated that ankyrin repeats of ANKRA2 and the paralogous bare lymphocyte syndrome transcription factor RFXANK recognize PxLPxL/I motifs shared by megalin, three histone deacetylases, and RFX5. We show here that that CCDC8 is a major partner of ANKRA2 but not RFXANK in cells. The CCDC8 gene is mutated in 3M syndrome, a short-stature disorder with additional facial and skeletal abnormalities. Two other genes mutated in this syndrome encode CUL7 and OBSL1. While CUL7 is a ubiquitin ligase and OBSL1 associates with the cytoskeleton, little is known about CCDC8. Binding and structural analyses reveal that the ankyrin repeats of ANKRA2 recognize a PxLPxL motif at the C-terminal region of CCDC8. The N-terminal part interacts with OBSL1 to form a CUL7 ligase complex. These results link ANKRA2 unexpectedly to 3M syndrome and suggest novel regulatory mechanisms for histone deacetylases and RFX7.


  • Organizational Affiliation
    • The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada; Department of Breast Cancer, The Third Affiliated Hospital, Kunming Medical University, Yunnan 650118, China.

Macromolecule Content 

  • Total Structure Weight: 20.86 kDa 
  • Atom Count: 1,389 
  • Modeled Residue Count: 176 
  • Deposited Residue Count: 190 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ankyrin repeat family A protein 2173Homo sapiensMutation(s): 0 
Gene Names: ANKRA2ANKRA
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9E1 (Homo sapiens)
Explore Q9H9E1 
Go to UniProtKB:  Q9H9E1
PHAROS:  Q9H9E1
GTEx:  ENSG00000164331 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9E1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 817Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0W5 (Homo sapiens)
Explore Q9H0W5 
Go to UniProtKB:  Q9H0W5
PHAROS:  Q9H0W5
GTEx:  ENSG00000169515 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0W5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.726α = 90
b = 49.791β = 98.23
c = 41.243γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description