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- EMDB-24173: Cryo-EM structure of the human SSU processome, state post-A1 - UT... -

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Basic information

Entry
Database: EMDB / ID: EMD-24173
TitleCryo-EM structure of the human SSU processome, state post-A1 - UTPC-central focused map
Map data
SampleHuman SSU processome, state post-A1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsVanden Broeck A / Singh S / Klinge S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
European Molecular Biology Organization (EMBO)ALTF 711-2019
CitationJournal: Science / Year: 2021
Title: Nucleolar maturation of the human small subunit processome.
Authors: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge /
Abstract: [Figure: see text].
History
DepositionJun 4, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24173.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 560 pix.
= 604.8 Å
1.08 Å/pix.
x 560 pix.
= 604.8 Å
1.08 Å/pix.
x 560 pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0317 / Movie #1: 0.0317
Minimum - Maximum-0.14593878 - 0.3108349
Average (Standard dev.)6.211839e-05 (±0.002224569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 604.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.1460.3110.000

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Supplemental data

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Segmentation: #1

Fileemd_24173_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_24173_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_24173_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_24173_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Human SSU processome, state post-A1

EntireName: Human SSU processome, state post-A1 / Number of Components: 1

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Component #1: protein, Human SSU processome, state post-A1

ProteinName: Human SSU processome, state post-A1 / Recombinant expression: No
MassTheoretical: 5 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 283 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 58 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 0.01 mm / Imaging Mode: BRIGHT FIELD / Defocus: 700.0 - 2700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of Digital Images: 84904

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 345121
3D reconstructionSoftware: RELION / Resolution: 2.6 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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