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- EMDB-55580: RNA polymerase II bound to Gdown1 and RPAP2 (RPAP2 map) -

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Basic information

Entry
Database: EMDB / ID: EMD-55580
TitleRNA polymerase II bound to Gdown1 and RPAP2 (RPAP2 map)
Map dataUnsharpened map, filtered to 4A resolution
Sample
  • Complex: RNA polymerase II bound to Gdown1 and RPAP2
    • Complex: RNA polymerase II
Keywordscytoplasm / polymerase / biogenesis / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55580.png

Downloads & links

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Map

FileDownload / File: emd_55580.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map, filtered to 4A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 384 pix.
= 503.808 Å		1.31 Å/pix.
x 384 pix.
= 503.808 Å		1.31 Å/pix.
x 384 pix.
= 503.808 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.04607632 - 0.12777953
Average (Standard dev.)0.000056639594 (±0.0029044624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 503.808 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55580_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Unsharpened map

Fileemd_55580_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

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Additional map: B-factor sharpened map

Fileemd_55580_additional_2.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_55580_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_55580_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : RNA polymerase II bound to Gdown1 and RPAP2

EntireName: RNA polymerase II bound to Gdown1 and RPAP2
Components
  • Complex: RNA polymerase II bound to Gdown1 and RPAP2
    • Complex: RNA polymerase II

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Supramolecule #1: RNA polymerase II bound to Gdown1 and RPAP2

SupramoleculeName: RNA polymerase II bound to Gdown1 and RPAP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Details: Complex isolated from cytoplasmic extract through a tag on endogenously expressed Gdown1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 520 KDa

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)

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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

Details: pH at 4 degrees Celsius
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 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: 3.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000
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: Warp (ver. 1.0.9), RELION (ver. 3.1), RELION (ver. 5.0))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

3218

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), RELION (ver. 5.0)) / Number images used: 54739
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software: (Name: RELION (ver. 3.1), RELION (ver. 5.0))
FSC plot (resolution estimation)

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