9DTG

The cryo-EM structure of apo KBTBD4

PDB DOI: https://doi.org/10.2210/pdb9DTG/pdb
EM Map EMD-47155: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-09-30 Released: 2024-11-27
Deposition Author(s): Xie, X., Mao, H., Liau, B., Zheng, N.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes

Zheng, N., Liau, B., Xie, X.

To be published.

Macromolecule Content

Total Structure Weight: 119.94 kDa
Atom Count: 8,069
Modelled Residue Count: 1,023
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Kelch repeat and BTB domain-containing protein 4	A, B	534	Homo sapiens	Mutation(s): 0 Gene Names: KBTBD4, BKLHD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVX7 (Homo sapiens) Explore Q9NVX7 Go to UniProtKB: Q9NVX7
PHAROS: Q9NVX7 GTEx: ENSG00000123444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NVX7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.