NMR Solution Structures of Human KAP1 PHD finger-bromodomain

Experimental Data Snapshot

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

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Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing

Zeng, L.Yap, K.L.Ivanov, A.V.Wang, X.Mujtaba, S.Plotnikova, O.Rauscher, F.J.Zhou, M.M.

(2008) Nat Struct Mol Biol 15: 626-633

  • DOI: https://doi.org/10.1038/nsmb.1416
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The tandem PHD finger-bromodomain, found in many chromatin-associated proteins, has an important role in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). Here we report the three-dimensional solution structure of the tandem PHD finger-bromodomain of KAP1. The structure reveals a distinct scaffold unifying the two protein modules, in which the first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other. A comprehensive mutation-based structure-function analysis correlating transcriptional repression, ubiquitin-conjugating enzyme 9 (UBC9) binding and SUMOylation shows that the PHD finger and the bromodomain of KAP1 cooperate as one functional unit to facilitate lysine SUMOylation, which is required for KAP1 co-repressor activity in gene silencing. These results demonstrate a previously unknown unified function for the tandem PHD finger-bromodomain as an intramolecular small ubiquitin-like modifier (SUMO) E3 ligase for transcriptional silencing.

  • Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, 1425 Madison Avenue, New York, New York 10029, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription intermediary factor 1-beta189Homo sapiensMutation(s): 0 
Gene Names: TRIM28KAP1RNF96TIF1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q13263 (Homo sapiens)
Explore Q13263 
Go to UniProtKB:  Q13263
PHAROS:  Q13263
GTEx:  ENSG00000130726 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13263
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
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: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations