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- EMDB-75415: PDB 10RN EMD-75411 Human RNase PNK bound to ATPyS ligand consensu... -

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Basic information

Entry
Database: EMDB / ID: EMD-75415
TitlePDB 10RN EMD-75411 Human RNase PNK bound to ATPyS ligand consensus EM map
Map dataConsensus map
Sample
  • Complex: Human RNase PNK bound to ATPyS ligand
KeywordsRibonuclease / Kinase / RNA / HEPN / LAS1L / NOL9 / ITS2 / Rixosome / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGordon J / Stanley RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural insights into RNA phosphorylation by the RNase PNK module of the human rixosome complex.
Authors: Jacob Gordon / Savannah M Seely / Huanchen Wang / Juno M Krahn / Wyatt A Peele / Mario J Borgnia / Alan J Warren / Robin E Stanley /
Abstract: The mammalian rixosome complex is a large multi-subunit complex that plays essential roles in ribosome assembly and heterochromatin maintenance. Three structural proteins form the stable core of the ...The mammalian rixosome complex is a large multi-subunit complex that plays essential roles in ribosome assembly and heterochromatin maintenance. Three structural proteins form the stable core of the rixosome to which three enzymatic modules are flexibly tethered including an RNA processing module, AAA-ATPase, and SUMO protease. The RNA processing module is formed by RNase PNK, a tetrameric assembly comprising two copies each of the LAS1L endoribonuclease (RNase) and the NOL9 polynucleotide kinase (PNK). Using single particle cryo-EM, we determined ATPγS and AMP-PNP/RNA-bound structures of human RNase PNK. The structures revealed the overall butterfly-like architecture of the complex and provide new insights into the mechanism of RNA accommodation and 5' hydroxyl phosphorylation within the NOL9 active site. Through reconstitution studies and molecular modeling, we establish how RNase PNK is incorporated into the larger rixosome complex by a distinct domain of LAS1L. Finally, we show that the human 5'-3' exoribonuclease XRN2 directly associates with RNase PNK and selectively degrades NOL9-phosphorylated RNA in vitro, thereby linking ITS2 processing by the rixosome to processive exonucleolytic decay. Collectively this work establishes an updated model for how the rixosome integrates its diverse enzymatic activities to regulate ITS2 processing.
History
DepositionFeb 4, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75415.png

Downloads & links

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Map

FileDownload / File: emd_75415.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.1623325 - 3.26054
Average (Standard dev.)-0.0013720309 (±0.046924904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Consensus half map A

Fileemd_75415_half_map_1.map
AnnotationConsensus half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus half map B

Fileemd_75415_half_map_2.map
AnnotationConsensus half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human RNase PNK bound to ATPyS ligand

EntireName: Human RNase PNK bound to ATPyS ligand
Components
  • Complex: Human RNase PNK bound to ATPyS ligand

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Supramolecule #1: Human RNase PNK bound to ATPyS ligand

SupramoleculeName: Human RNase PNK bound to ATPyS ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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