8U80

KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD)

PDB DOI: https://doi.org/10.2210/pdb8U80/pdb
EM Map EMD-41995: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-15 Released: 2023-10-11
Deposition Author(s): Kuntz, D.A., Nguyen, D.M., Narayanan, N., Prive, G.G.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex

Nguyen, D.M., Rath, D.H., Devost, D., Petrin, D., Rizk, R., Ji, A.X., Narayanan, N., Yong, D., Zhai, A., Kuntz, D.A., Mian, M.U.Q., Pomroy, N.C., Keszei, A.F.E., Benlekbir, S., Mazhab-Jafari, M.T., Rubinstein, J.L., Hebert, T.E., Prive, G.G.

(2024) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.2315018121

Macromolecule Content

Total Structure Weight: 353.3 kDa
Atom Count: 19,260
Modelled Residue Count: 2,360
Deposited Residue Count: 3,075
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BTB/POZ domain-containing protein KCTD5	A [auth K1], B [auth K2], C [auth K3], D [auth K4], E [auth K5]	234	Homo sapiens	Mutation(s): 0 Gene Names: KCTD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXV2 (Homo sapiens) Explore Q9NXV2 Go to UniProtKB: Q9NXV2
PHAROS: Q9NXV2 GTEx: ENSG00000167977
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NXV2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-3	F [auth C1], G [auth C2], H [auth C3], I [auth C4], J [auth C5]	381	Homo sapiens	Mutation(s): 0 Gene Names: CUL3, KIAA0617
UniProt & NIH Common Fund Data Resources
Find proteins for Q13618 (Homo sapiens) Explore Q13618 Go to UniProtKB: Q13618
PHAROS: Q13618 GTEx: ENSG00000036257
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13618
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2023-10-11
Type: Initial release
Version 1.1: 2023-10-25
Changes: Structure summary
Version 1.2: 2024-04-24
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.