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TitleCryo-EM structures of UBA6 reveal mechanisms of E1-E2 specificity and dual FAT10/ubiquitin thioester transfer.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateFeb 28, 2026
AuthorsDigant Nayak / Lijia Jia / Priscila Dos Santos Bury / Eliza A Ruben / Ankita Shukla / Anindita Nayak / Caleb M Stratton / Pirouz Ebadi / Hee Cho / Anna A Tumanova / Joyce T Varughese / Lingmin Yuan / Fei Gao / Kristin E Cano / Christopher Davies / Patrick Sung / Michaela U Gack / Elizabeth V Wasmuth / Shaun K Olsen /
PubMed AbstractUBA1 and UBA6 define parallel ubiquitin (Ub) activation systems that perform non-overlapping roles in Ub and ubiquitin-like protein (Ubl) signaling. Whereas UBA1 supports the canonical Ub pathway, ...UBA1 and UBA6 define parallel ubiquitin (Ub) activation systems that perform non-overlapping roles in Ub and ubiquitin-like protein (Ubl) signaling. Whereas UBA1 supports the canonical Ub pathway, UBA6 also activates the Ubl FAT10, linking Ub signaling to immune-regulated proteostasis. In addition to selective Ub/Ubl activation, UBA1 and UBA6 engage distinct sets of E2s, yet how these enzymes achieve selective E2 engagement has remained unclear. Using chemical trapping and high-resolution cryo-EM, we determine four structures of UBA6-E2 complexes representing the thioester-transfer step with either FAT10 or Ub, revealing how this E1 distinguishes its cognate partners. UBA6 achieves E2 specificity through coordinated contributions of the UFD and SCCH domains, a dual-domain mechanism that contrasts with the UFD-dominated selectivity of UBA1. The structures further show that an existing inositol hexakisphosphate (InsP₆)-binding site, unique to UBA6, stabilizes an expanded SCCH cleft that pre-organizes the enzyme for selective engagement of UBA6-specific E2s. These findings define principles for E1-E2 recognition and identify InsP₆ as a cofactor shaping specificity within the Ub-like conjugation network.
External linksNat Commun / PubMed:41764162 / PubMed Central
MethodsEM (single particle)
Resolution2.73 - 3.86 Å
Structure data

73059

9ykv

EMDB-73059, PDB-9ykv:
Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic complex.
Method: EM (single particle) / Resolution: 2.73 Å

73060

9ykw

EMDB-73060, PDB-9ykw:
Cryo-EM structure of double-loaded human UBA6-UBE2Z-Ub(t)/Ub(a) thioester mimetic complex.
Method: EM (single particle) / Resolution: 3.86 Å

73079

9ylb

EMDB-73079, PDB-9ylb:
Cryo-EM structure of single-loaded human UBA6-UBE2Z/FAT10(a) adenylate complex.
Method: EM (single particle) / Resolution: 3.24 Å

73081

9ylf

EMDB-73081, PDB-9ylf:
Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex.
Method: EM (single particle) / Resolution: 3.14 Å

Chemicals

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

ChemComp-POP:
PYROPHOSPHATE 2-

Source
  • homo sapiens (human)
KeywordsTRANSFERASE/Ligase / E1 E2 enzymes / TRANSFERASE / TRANSFERASE-Ligase complex

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