6QAJ

Structure of the tripartite motif of KAP1/TRIM28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 116: 15042-15051

  • DOI: 10.1073/pnas.1901318116

  • 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 recogn ...

    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.,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom.,Biophysics Facility, MRC-LMB, CB2 0QH Cambridge, United Kingdom.,X-ray Crystallography Facility, MRC-LMB, CB2 0QH Cambridge, United Kingdom.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom; ymodis@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Transcription intermediary factor 1-beta
A, B
544Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 0 
Gene Names: TRIM28 (KAP1, RNF96, TIF1B), E
EC: 3.2.1.17
Find proteins for Q13263 (Homo sapiens)
Go to Gene View: TRIM28
Go to UniProtKB:  Q13263
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 59.774α = 90.00
b = 169.332β = 90.00
c = 374.508γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction
RESOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references