6QAJ

Structure of the tripartite motif of KAP1/TRIM28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


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 U S A 116: 15042-15051

  • DOI: 10.1073/pnas.1901318116
  • Structures With Same Primary Citation

  • 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

    Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Transcription intermediary factor 1-beta
A, B
544Escherichia virus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 3.2.1.17 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for Q13263 (Homo sapiens)
Go to UniProtKB:  Q13263
NIH Common Fund Data Resources
PHAROS  Q13263
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: C 2 2 21
  • Diffraction Data DOI: 10.15785/SBGRID/637 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.774α = 90
b = 169.332β = 90
c = 374.508γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
RESOLVEphasing
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 

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