8U81

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

• PDB DOI: https://doi.org/10.2210/pdb8U81/pdb
• EM Map EMD-41996: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): Yes 


• 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)

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Experimental Data Snapshot

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

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A5B5C5D5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - B5 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - D5 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Hetero 10-mer - A5C5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

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

Macromolecules

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]	233	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 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	K [auth B1], L [auth B2], M [auth B3], N [auth B4], O [auth B5]	340	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	P [auth G1], Q [auth G2], R [auth G3], S [auth G4], T [auth G5]	71	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.20.1-4487
MODEL REFINEMENT	NAMD	2.14
MODEL REFINEMENT	VMD	1.93

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Kuntz, D.A., Nguyen, D.M., Narayanan, N., Prive, G.G.

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

Revision History  

• 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