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Structure paper

TitleStructure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 17, Page e2315018121, Year 2024
Publish dateApr 23, 2024
AuthorsDuc Minh Nguyen / Deanna H Rath / Dominic Devost / Darlaine Pétrin / Robert Rizk / Alan X Ji / Naveen Narayanan / Darren Yong / Andrew Zhai / Douglas A Kuntz / Maha U Q Mian / Neil C Pomroy / Alexander F A Keszei / Samir Benlekbir / Mohammad T Mazhab-Jafari / John L Rubinstein / Terence E Hébert / Gilbert G Privé /
PubMed AbstractHeterotrimeric 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- ...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) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3/Gβγ assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5/CUL3 and KCTD5/Gβγ moieties of the structure. CRL3 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/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.
External linksProc Natl Acad Sci U S A / PubMed:38625940 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 5.7 Å
Structure data

41994

8u7z

EMDB-41994: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(CTD)/Gbeta1gamma2
PDB-8u7z: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(CTD)/Gbeta1gamma2
Method: EM (single particle) / Resolution: 2.97 Å

41995

8u80

EMDB-41995: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinement of KCTD5(BTB)/Cullin3(NTD)
PDB-8u80: KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD)
Method: EM (single particle) / Resolution: 3.6 Å

41996

8u81

EMDB-41996: KCTD5/Cullin3/Gbeta1gamma2 Complex State A: Composite Map from RELION Multi-body Refinement
PDB-8u81: KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-41997: KCTD5/Cullin3/Gbeta1gamma2 Complex State A: Reference Map for Composite Map EMD-41996
Method: EM (single particle) / Resolution: 3.96 Å

EMDB-41998: KCTD5/Cullin3/Gbeta1gamma2 Complex State A Body 1: RELION Multi-body Refinement of KCTD5(CTD)/Gbeta1gamma2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-41999: KCTD5/Cullin3/Gbeta1gamma2 Complex State A Body 2: RELION Multi-body Refinemnent of KCTD5(BTB)/Cullin3(NTD)
Method: EM (single particle) / Resolution: 5.7 Å

42000

8u82

EMDB-42000: KCTD5/Cullin3/Gbeta1gamma2 Complex State B: Composite Map from RELION Multi-body Refinement
PDB-8u82: KCTD5/Cullin3/Gbeta1gamma2 Complex: State B From Composite RELION Multi-body Refinement Map
Method: EM (single particle) / Resolution: 3.83 Å

EMDB-42001: KCTD5/Cullin3/Gbeta1gamma2 Complex State B: Reference Map for Composite Map EMD-42000
Method: EM (single particle) / Resolution: 3.96 Å

EMDB-42002: KCTD5/Cullin3/Gbeta1gamma2 Complex State B Body 1: RELION Multi-body Refinement of KCTD5(CTD)/Gbeta1gamma2
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-42003: KCTD5/Cullin3/Gbeta1gamma2 Complex State B Body 2: RELION Multi-body Refinement of KCTD5(BTB)/Cullin3(NTD)
Method: EM (single particle) / Resolution: 4.2 Å

42004

8u83

EMDB-42004: KCTD5/Cullin3/Gbeta1gamma2 Complex State C: Composite Map from RELION Multi-body Refinement
PDB-8u83: KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement Map
Method: EM (single particle) / Resolution: 3.97 Å

EMDB-42005: KCTD5/Cullin3/Gbeta1gamma2 Complex State C: Reference Map for Composite Map EMD-42004
Method: EM (single particle) / Resolution: 3.97 Å

EMDB-42006: KCTD5/Cullin3/Gbeta1gamma2 Complex State C Body 1: RELION Multi-body Refinement of KCTD5(CTD)/Gbeta1gamma2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-42007: KCTD5/Cullin3/Gbeta1gamma2 Complex State C Body 2: RELION Multi-body Refinement of KCTD5(BTB)/Cullin3(NTD)
Method: EM (single particle) / Resolution: 4.3 Å

42008

8u84

EMDB-42008: KCTD5/Cullin3/Gbeta1gamma2 Complex State D: Composite Map from RELION Multi-body Refinement
PDB-8u84: KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map
Method: EM (single particle) / Resolution: 3.88 Å

EMDB-42009: KCTD5/Cullin3/Gbeta1gamma2 Complex State D: Reference Map for Composite Map EMD-42008
Method: EM (single particle) / Resolution: 3.98 Å

EMDB-42010: KCTD5/Cullin3/Gbeta1gamma2 Complex State D Body 1: RELION Multi-body Refinement of KCTD5(CTD)/Gbeta1gamma2
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-42011: KCTD5/Cullin3/Gbeta1gamma2 Complex State D Body 2: RELION Multi-body Refinemnent of KCTD5(BTB)/Cullin3(NTD)
Method: EM (single particle) / Resolution: 4.2 Å

Source
  • homo sapiens (human)
KeywordsLIGASE / cullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process

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