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 1IXD | pdb_00001ixd

Solution structure of the CAP-GLY domain from human cylindromatosis tomour-suppressor CYLD


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKgamma

Saito, K., Kigawa, T., Koshiba, S., Sato, K., Matsuo, Y., Sakamoto, A., Takagi, T., Shirouzu, M., Yabuki, T., Nunokawa, E., Seki, E., Matsuda, T., Aoki, M., Miyata, Y., Hirakawa, N., Inoue, M., Terada, T., Nagase, T., Kikuno, R., Nakayama, M., Ohara, O., Tanaka, A., Yokoyama, S.

(2004) Structure 12: 1719-1728

  • DOI: https://doi.org/10.1016/j.str.2004.07.012
  • Primary Citation Related Structures: 
    1IXD

  • PubMed Abstract: 

    CYLD was originally identified as the human familial cylindromatosis tumor suppressor. Recently, it was reported that CYLD directly interacts with NEMO/IKKgamma and TRAF2 in the NF-kappaB signaling pathway. The two proteins bind to a region of CYLD that contains a Cys-box motif and the third cytoskeleton-associated protein-glycine conserved (CAP-Gly) domain. Here we report that the third CAP-Gly domain of CYLD specifically interacts with one of the two proline-rich sequences of NEMO/IKKgamma. The tertiary structure of the CAP-Gly domain shares the five-stranded beta sheet topology with the SH3 domain, which is well known as a proline-rich sequence-recognition domain. However, chemical shift mapping revealed that the peptide binding site of the CAP-Gly domain is formed without the long peptide binding loop characteristic of the SH3 domain. Therefore, CAP-Gly is likely to be a novel proline-rich sequence binding domain with a mechanism different from that of the SH3 domain.


  • Organizational Affiliation: 
    • RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 10.87 kDa 
  • Atom Count: 762 
  • Modeled Residue Count: 104 
  • Deposited Residue Count: 104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cylindromatosis tumour-suppressor CYLD104Homo sapiensMutation(s): 0 
Gene Names: fh04363
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQC7 (Homo sapiens)
Explore Q9NQC7 
Go to UniProtKB:  Q9NQC7
PHAROS:  Q9NQC7
GTEx:  ENSG00000083799 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQC7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection