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TitleStructure of cytoplasmic RNA polymerase II.
Journal, issue, pagesNat Commun, Year 2026
Publish dateJul 13, 2026
AuthorsAnnamaria Hlavata / Benjamin Neuditschko / Ulla Schellhaas / Clemens Plaschka / Franz Herzog / Carrie Bernecky /
PubMed AbstractRNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how ...RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated assembly factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contains Gdown1 and three biogenesis factors - RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis reveals how RPAP2 tethers GPN1-GPN3 to the complex and how the assembly of the RPAP2-GPN1-GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a molecular switch regulating biogenesis factor association, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes.
External linksNat Commun / PubMed:42443208
MethodsEM (single particle)
Resolution2.7 - 3.3 Å
Structure data

EMDB-55578: RNA polymerase II bound to Gdown1 and RPAP2 (Pol II core map)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-55579: RNA polymerase II bound to Gdown1 and RPAP2 (Pol II stalk map)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-55580: RNA polymerase II bound to Gdown1 and RPAP2 (RPAP2 map)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-55581: RNA polymerase II bound to Gdown1 and RPAP2 (Gdown1 N-terminus map)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-55582: RNA polymerase II bound to Gdown1 and RPAP2 (Gdown1 C-terminus map)
Method: EM (single particle) / Resolution: 2.8 Å

55583

9t5h

EMDB-55583: RNA polymerase II bound to Gdown1 and RPAP2 (composite map)
PDB-9t5h: RNA polymerase II bound to Gdown1 and RPAP2
Method: EM (single particle) / Resolution: 2.7 Å

55585

9t5j

EMDB-55585, PDB-9t5j:
RPAP2-GPN1-GPN3 complex (GDP-bound)
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsTRANSCRIPTION / cytoplasm / polymerase / biogenesis

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