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- EMDB-75418: PDB 10RR EMD-75414 Human RNase PNK bound to AMPPNP ligand + rCAA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75418
TitlePDB 10RR EMD-75414 Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site consensus EM map
Map dataConsensus EM map
Sample
  • Complex: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
KeywordsRibonuclease / Kinase / RNA / HEPN / LAS1L / NOL9 / ITS2 / Rixosome / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 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: To Be Published
Title: Structural Insights into RNA Phosphorylation by the RNase PNK Module of the Human Rixosome Complex.
Authors: Gordon J / Stanley RE
History
DepositionFeb 4, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75418.png

Downloads & links

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Map

FileDownload / File: emd_75418.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 504 pix.
= 332.64 Å		0.66 Å/pix.
x 504 pix.
= 332.64 Å		0.66 Å/pix.
x 504 pix.
= 332.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.67165923 - 0.84191823
Average (Standard dev.)0.00010112525 (±0.011555994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 332.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Consensus half map A

Fileemd_75418_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_75418_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 AMPPNP ligand + rCAA in PNK active site

EntireName: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
Components
  • Complex: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site

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Supramolecule #1: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site

SupramoleculeName: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88000
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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