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- PDB-9t5j: RPAP2-GPN1-GPN3 complex (GDP-bound) -

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Basic information

Entry
Database: PDB / ID: 9t5j
TitleRPAP2-GPN1-GPN3 complex (GDP-bound)
Components
  • GPN-loop GTPase 1
  • GPN-loop GTPase 3
  • Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
KeywordsTRANSCRIPTION / cytoplasm / polymerase / biogenesis
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / PERK-mediated unfolded protein response / transcription preinitiation complex / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / protein import into nucleus ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / PERK-mediated unfolded protein response / transcription preinitiation complex / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / protein import into nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / nucleolus / GTP binding / protein-containing complex / nucleoplasm / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GPN-loop GTPase 3 / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / GPN-loop GTPase 1 / GPN-loop GTPase core domain profile. / GPN-loop GTPase / Conserved hypothetical ATP binding protein ...GPN-loop GTPase 3 / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / GPN-loop GTPase 1 / GPN-loop GTPase core domain profile. / GPN-loop GTPase / Conserved hypothetical ATP binding protein / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 / GPN-loop GTPase 1 / GPN-loop GTPase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHlavata, A. / Bernecky, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structure of cytoplasmic RNA polymerase II.
Authors: Annamaria Hlavata / Benjamin Neuditschko / Ulla Schellhaas / Clemens Plaschka / Franz Herzog / Carrie Bernecky /
Abstract: 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 ...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.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
B: GPN-loop GTPase 1
C: GPN-loop GTPase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4287
Polymers144,4933
Non-polymers9354
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 / RNA polymerase II-associated protein 2


Mass: 69768.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPAP2, C1orf82 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8IXW5, protein-serine/threonine phosphatase
#2: Protein GPN-loop GTPase 1 / MBD2-interacting protein / MBDin / RNAPII-associated protein 4 / XPA-binding protein 1


Mass: 41934.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPN1, MBDIN, RPAP4, XAB1, HUSSY-23 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9HCN4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Protein GPN-loop GTPase 3 / ATP-binding domain 1 family member C


Mass: 32790.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPN3, ATPBD1C, AD-009, UNQ1876/PRO4319 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UHW5
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1RPAP2-GPN1-GPN3 complexCOMPLEXReconstituted complex formed by addition of purified RPAP2 to purified GPN1-GPN3#1-#30RECOMBINANT
2GPN1-GPN3COMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.14 MDaNO
210.075 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8.2 / Details: pH at 4 degrees Celsius
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
32 mMmagnesium chlorideMgCl21
42 mMdithiothreitolC4H10O2S21
510 uMzinc chlorideZnCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 mA current, 7.0 x 10-1 mbar vacuum / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.16 sec. / Electron dose: 80.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPU2.11image acquisition
4CTFFIND4-1CTF correction
7UCSF ChimeraX1.1model fitting
8ISOLDE1.10.1model fitting
10cryoSPARC4.7.0initial Euler assignment
11RELION5final Euler assignment
13RELION53D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 532839 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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