9B9V | pdb_00009b9v

Cryo-EM structure of the ZBTB9 BTB domain filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9B9V

This is version 1.0 of the entry. See complete history

Literature

Polymerization of ZBTB transcription factors regulates chromatin occupancy.

Park, P.M.C.Park, J.Brown, J.Hunkeler, M.Roy Burman, S.S.Donovan, K.A.Yoon, H.Nowak, R.P.Slabicki, M.Ebert, B.L.Fischer, E.S.

(2024) Mol Cell 84: 2511-2524.e8

  • DOI: https://doi.org/10.1016/j.molcel.2024.06.010
  • Primary Citation Related Structures: 
    9B9R, 9B9V

  • PubMed Abstract: 

    BCL6, an oncogenic transcription factor (TF), forms polymers in the presence of a small-molecule molecular glue that stabilizes a complementary interface between homodimers of BCL6's broad-complex, tramtrack, and bric-à-brac (BTB) domain. The BTB domains of other proteins, including a large class of TFs, have similar architectures and symmetries, raising the possibility that additional BTB proteins self-assemble into higher-order structures. Here, we surveyed 189 human BTB proteins with a cellular fluorescent reporter assay and identified 18 ZBTB TFs that show evidence of polymerization. Through biochemical and cryoelectron microscopy (cryo-EM) studies, we demonstrate that these ZBTB TFs polymerize into filaments. We found that BTB-domain-mediated polymerization of ZBTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites, leading to repression of target genes. Our results reveal a role of higher-order structures in regulating ZBTB TFs and suggest an underappreciated role for TF polymerization in modulating gene expression.


  • Organizational Affiliation
    • Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Macromolecule Content 

  • Total Structure Weight: 271.43 kDa 
  • Atom Count: 13,412 
  • Modeled Residue Count: 1,708 
  • Deposited Residue Count: 2,464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger and BTB domain-containing protein 9
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
176Homo sapiensMutation(s): 0 
Gene Names: ZBTB9
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C00 (Homo sapiens)
Explore Q96C00 
Go to UniProtKB:  Q96C00
PHAROS:  Q96C00
GTEx:  ENSG00000213588 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96C00
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release