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 8U81 | pdb_00008u81

KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8U81

This is version 1.3 of the entry. See complete history. 

Literature

Structure and dynamics of a pentameric KCTD5/CUL3/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.A., Benlekbir, S., Mazhab-Jafari, M.T., Rubinstein, J.L., Hebert, T.E., Prive, G.G.

(2024) Proc Natl Acad Sci U S A 121: e2315018121-e2315018121

  • DOI: https://doi.org/10.1073/pnas.2315018121
  • Primary Citation Related Structures: 
    8U7Z, 8U80, 8U81, 8U82, 8U83, 8U84

  • PubMed Abstract: 

    Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3 KCTD5 ) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3 NTD /Gβ 1 γ 2 assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5 BTB /CUL3 NTD and KCTD5 CTD /Gβγ moieties of the structure. CRL3 KCTD5 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3 NTD /Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.


  • Organizational Affiliation: 
    • Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.

Macromolecule Content 

  • Total Structure Weight: 578.96 kDa 
  • Atom Count: 37,890 
  • Modeled Residue Count: 4,770 
  • Deposited Residue Count: 5,125 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BTB/POZ domain-containing protein KCTD5A [auth K1],
B [auth K2],
C [auth K3],
D [auth K4],
E [auth K5]
233Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXV2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cullin-3F [auth C1],
G [auth C2],
H [auth C3],
I [auth C4],
J [auth C5]
381Homo sapiensMutation(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
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UniProt GroupQ13618
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1K [auth B1],
L [auth B2],
M [auth B3],
N [auth B4],
O [auth B5]
340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2P [auth G1],
Q [auth G2],
R [auth G3],
S [auth G4],
T [auth G5]
71Homo sapiensMutation(s): 1 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTNAMD2.14
MODEL REFINEMENTVMD1.93

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
  • Version 1.3: 2024-05-01
    Changes: Database references