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- EMDB-55585: RPAP2-GPN1-GPN3 complex (GDP-bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-55585
TitleRPAP2-GPN1-GPN3 complex (GDP-bound)
Map dataB-factor -50 sharpened map
Sample
  • Complex: RPAP2-GPN1-GPN3 complex
    • Complex: GPN1-GPN3
      • Protein or peptide: GPN-loop GTPase 1
      • Protein or peptide: GPN-loop GTPase 3
    • Protein or peptide: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordscytoplasm / polymerase / biogenesis / TRANSCRIPTION
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
Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 / GPN-loop GTPase 1 / GPN-loop GTPase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHlavata A / Bernecky C
Funding support1 items
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, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55585.png

Downloads & links

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Map

FileDownload / File: emd_55585.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor -50 sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 320 pix.
= 256.512 Å		0.8 Å/pix.
x 320 pix.
= 256.512 Å		0.8 Å/pix.
x 320 pix.
= 256.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8016 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.014972317 - 0.031332742
Average (Standard dev.)0.0000027492904 (±0.0006756035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 256.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_55585_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer-processed map

Fileemd_55585_additional_2.map
AnnotationDeepEMhancer-processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_55585_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_55585_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : RPAP2-GPN1-GPN3 complex

EntireName: RPAP2-GPN1-GPN3 complex
Components
  • Complex: RPAP2-GPN1-GPN3 complex
    • Complex: GPN1-GPN3
      • Protein or peptide: GPN-loop GTPase 1
      • Protein or peptide: GPN-loop GTPase 3
    • Protein or peptide: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RPAP2-GPN1-GPN3 complex

SupramoleculeName: RPAP2-GPN1-GPN3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Reconstituted complex formed by addition of purified RPAP2 to purified GPN1-GPN3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75 KDa

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Supramolecule #2: GPN1-GPN3

SupramoleculeName: GPN1-GPN3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

MacromoleculeName: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.768938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPMADFAGPS SAGRKAGAPR CSRKAAGTKQ TSTLKQEDAS KRKAELEAAV RKKIEFERKA LHIVEQLLEE NITEEFLMEC GRFITPAHY SDVVDERSIV KLCGYPLCQK KLGIVPKQKY KISTKTNKVY DITERKSFCS NFCYQASKFF EAQIPKTPVW V REEERHPD ...String:
GPMADFAGPS SAGRKAGAPR CSRKAAGTKQ TSTLKQEDAS KRKAELEAAV RKKIEFERKA LHIVEQLLEE NITEEFLMEC GRFITPAHY SDVVDERSIV KLCGYPLCQK KLGIVPKQKY KISTKTNKVY DITERKSFCS NFCYQASKFF EAQIPKTPVW V REEERHPD FQLLKEEQSG HSGEEVQLCS KAIKTSDIDN PSHFEKQYES SSSSTHSDSS SDNEQDFVSS ILPGNRPNST NI RPQLHQK SIMKKKAGHK ANSKHKDKEQ TVVDVTEQLG DCKLDSQEKD ATCELPLQKV NTQSSSNSTL PERLKASENS ESE YSRSEI TLVGISKKSA EHFKRKFAKS NQVSRSVSSS VQVCPEVGKR NLLKVLKETL IEWKTEETLR FLYGQNYASV CLKP EASLV KEELDEDDII SDPDSHFPAW RESQNSLDES LPFRGSGTAI KPLPSYENLK KETEKLNLRI REFYRGRYVL GEETT KSQD SEEHDSTFPL IDSSSQNQIR KRIVLEKLSK VLPGLLVPLQ ITLGDIYTQL KNLVRTFRLT NRNIIHKPAE WTLIAM VLL SLLTPILGIQ KHSQEGMVFT RFLDTLLEEL HLKNEDLESL TIIFRTSCLP E

UniProtKB: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

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Macromolecule #2: GPN-loop GTPase 1

MacromoleculeName: GPN-loop GTPase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.934152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPMAASAAAA ELQASGGPRH PVCLLVLGMA GSGKTTFVQR LTGHLHAQGT PPYVINLDPA VHEVPFPANI DIRDTVKYKE VMKQYGLGP NGGIVTSLNL FATRFDQVMK FIEKAQNMSK YVLIDTPGQI EVFTWSASGT IITEALASSF PTVVIYVMDT S RSTNPVTF ...String:
GPMAASAAAA ELQASGGPRH PVCLLVLGMA GSGKTTFVQR LTGHLHAQGT PPYVINLDPA VHEVPFPANI DIRDTVKYKE VMKQYGLGP NGGIVTSLNL FATRFDQVMK FIEKAQNMSK YVLIDTPGQI EVFTWSASGT IITEALASSF PTVVIYVMDT S RSTNPVTF MSNMLYACSI LYKTKLPFIV VMNKTDIIDH SFAVEWMQDF EAFQDALNQE TTYVSNLTRS MSLVLDEFYS SL RVVGVSA VLGTGLDELF VQVTSAAEEY EREYRPEYER LKKSLANAES QQQREQLERL RKDMGSVALD AGTAKDSLSP VLH PSDLIL TRGTLDEEDE EADSDTDDID HRVTEESHEE PAFQNFMQES MAQYWKRNNK

UniProtKB: GPN-loop GTPase 1

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Macromolecule #3: GPN-loop GTPase 3

MacromoleculeName: GPN-loop GTPase 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.790266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPRYAQLVMG PAGSGKSTYC ATMVQHCEAL NRSVQVVNLD PAAEHFNYSV MADIRELIEV DDVMEDDSLR FGPNGGLVFC MEYFANNFD WLENCLGHVE DDYILFDCPG QIELYTHLPV MKQLVQQLEQ WEFRVCGVFL VDSQFMVESF KFISGILAAL S AMISLEIP ...String:
MPRYAQLVMG PAGSGKSTYC ATMVQHCEAL NRSVQVVNLD PAAEHFNYSV MADIRELIEV DDVMEDDSLR FGPNGGLVFC MEYFANNFD WLENCLGHVE DDYILFDCPG QIELYTHLPV MKQLVQQLEQ WEFRVCGVFL VDSQFMVESF KFISGILAAL S AMISLEIP QVNIMTKMDL LSKKAKKEIE KFLDPDMYSL LEDSTSDLRS KKFKKLTKAI CGLIDDYSMV RFLPYDQSDE ES MNIVLQH IDFAIQYGED LEFKEPKERE DESSSMFDEY FQECQDE

UniProtKB: GPN-loop GTPase 3

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.2
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
2.0 mMMgCl2magnesium chloride
2.0 mMC4H10O2S2dithiothreitol
10.0 uMZnCl2zinc chloride

Details: pH at 4 degrees Celsius
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA current, 7.0 x 10-1 mbar vacuum
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
SoftwareName: EPU (ver. 2.11)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.16 sec. / Average electron dose: 80.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4-1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 532839
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.10)
Output model

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

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