7Z36 image
Deposition Date 2022-03-01
Release Date 2022-11-02
Last Version Date 2024-01-31
Entry Detail
PDB ID:
7Z36
Keywords:
Title:
Crystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Endolysin,Transcription intermediary factor 1-beta,Isoform 2 of Transcription intermediary factor 1-beta
Gene (Uniprot):E, TRIM28
Mutations:KAP1 B-box 1 domain (residues 141-202) deleted
Chain IDs:A, B
Chain Length:482
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:SMARCAD1 CUE1 domain
Chain IDs:C, E (auth: S)
Chain Length:73
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein 93
Gene (Uniprot):ZNF93
Chain IDs:D
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structure and functional mapping of the KRAB-KAP1 repressor complex.
Embo J. 41 e111179 e111179 (2022)
PMID: 36341546 DOI: 10.15252/embj.2022111179

Abstact

Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.

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Primary Citation of related structures