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- EMDB-72900: insect class II H/ACA snoRNP - Focused map 3'half -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72900
Titleinsect class II H/ACA snoRNP - Focused map 3'half
Map datafocused map 3' half
Sample
  • Complex: Insect H/ACA snoRNP
KeywordsPseudouridine synthase / enzyme complex / snoRNA / snoRNP / RNA BINDING PROTEIN
Biological speciesTrichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsPanwar HS / Worden EW
Funding support United States, Canada, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM147261-01 United States
Canadian Institutes of Health Research (CIHR)437623 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Interprotomer communication and functional asymmetry in H/ACA snoRNPs
Authors: Panwar HS / Vos T / Xie X / Jang HS / Lee H / Sheldon RD / Worden EJ / Kothe U
History
DepositionSep 26, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72900.png

Downloads & links

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Map

FileDownload / File: emd_72900.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused map 3' half
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0207
Minimum - Maximum-0.2583835 - 0.50495034
Average (Standard dev.)-0.00013922282 (±0.008850261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72900_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened Map

Fileemd_72900_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_72900_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_72900_half_map_2.map
AnnotationHalf 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 : Insect H/ACA snoRNP

EntireName: Insect H/ACA snoRNP
Components
  • Complex: Insect H/ACA snoRNP

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Supramolecule #1: Insect H/ACA snoRNP

SupramoleculeName: Insect H/ACA snoRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 733250
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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