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- EMDB-55042: Map of the SPATA5-SPATA5L1-CINP-C1ORF109 complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-55042
TitleMap of the SPATA5-SPATA5L1-CINP-C1ORF109 complex
Map data
Sample
  • Complex: SPATA5-SPATA5L1-CINP-C1ORF109 complex
    • Complex: SPATA5
    • Complex: SPATA5L1
    • Complex: CINP
    • Complex: C1ORF109
KeywordsATPase / coiled-coil / ribosome biogenesis factor / ribosome biogenesis / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.47 Å
AuthorsWeisser M / Masternak M / Montoya G
Funding support Denmark, European Union, 4 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF0024386 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF18OC0055061 Denmark
European Research Council (ERC)101096548European Union
CitationJournal: To Be Published
Title: The SPATA5-SPATA5L1-CINP-C1ORF109 complex is essential for cytoplasmic pre-60S ribosome maturation
Authors: Walter J / Weisser M / Masternak M / Wild T / Garcia-Martin R / Liebner T / Bragado-Nilsson E / Narita T / Zavogianni N / Montoya G / Choudhary C
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55042.png

Downloads & links

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Map

FileDownload / File: emd_55042.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.037341747 - 0.0999166
Average (Standard dev.)0.00012212119 (±0.006363735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55042_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55042_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SPATA5-SPATA5L1-CINP-C1ORF109 complex

EntireName: SPATA5-SPATA5L1-CINP-C1ORF109 complex
Components
  • Complex: SPATA5-SPATA5L1-CINP-C1ORF109 complex
    • Complex: SPATA5
    • Complex: SPATA5L1
    • Complex: CINP
    • Complex: C1ORF109

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Supramolecule #1: SPATA5-SPATA5L1-CINP-C1ORF109 complex

SupramoleculeName: SPATA5-SPATA5L1-CINP-C1ORF109 complex / type: complex / ID: 1 / Parent: 0
Details: 4 molecules of SPATA5, 2 molecules of SPATA5L1, 2 molecules of CINP, 2 molecules of C1ORF109
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23 kDa/nm

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Supramolecule #2: SPATA5

SupramoleculeName: SPATA5 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: SPATA5L1

SupramoleculeName: SPATA5L1 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: CINP

SupramoleculeName: CINP / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: C1ORF109

SupramoleculeName: C1ORF109 / type: complex / ID: 5 / Parent: 1
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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 3 / Number real images: 30000 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 54421
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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