Structure of the tripartite motif of KAP1/TRIM28

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report

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Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing.

Stoll, G.A.Oda, S.I.Chong, Z.S.Yu, M.McLaughlin, S.H.Modis, Y.

(2019) Proc Natl Acad Sci U S A 116: 15042-15051

  • DOI: https://doi.org/10.1073/pnas.1901318116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.

  • Organizational Affiliation

    Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin,Transcription intermediary factor 1-beta
A, B
544Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
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 GroupsP00720Q13263
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.774α = 90
b = 169.332β = 90
c = 374.508γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101908/Z/13/Z
Wellcome TrustUnited Kingdom205833/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description