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- EMDB-50816: Rea1 D2915A-R2976A-D3042A mutant ATP conformation I -

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Basic information

Entry
Database: EMDB / ID: EMD-50816
TitleRea1 D2915A-R2976A-D3042A mutant ATP conformation I
Map data
Sample
  • Organelle or cellular component: Rea1 monomer
KeywordsAAA+ protein / ribosome maturation / TRANSLOCASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsBusselez J / Schmidt H
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Nucleotide independent as well as ATP-hydrolysis driven steps of Rea1 Linker remodelling drive the removal of assembly factors from pre-ribosomal particles
Authors: Busselez J / Koenig G / Dominique C / Klos T / Velayudhan D / Sosnowski P / Marechal N / Crucifix C / Gizardin-Fredon H / Cianferani S / Benjamin A / Henry Y / Henras A / Schmidt H
History
DepositionJun 28, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50816.png

Downloads & links

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Map

FileDownload / File: emd_50816.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 128 pix.
= 440.32 Å		3.44 Å/pix.
x 128 pix.
= 440.32 Å		3.44 Å/pix.
x 128 pix.
= 440.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.5613291 - 0.914676
Average (Standard dev.)0.0009034416 (±0.015838107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50816_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50816_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 : Rea1 monomer

EntireName: Rea1 monomer
Components
  • Organelle or cellular component: Rea1 monomer

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Supramolecule #1: Rea1 monomer

SupramoleculeName: Rea1 monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 500 KDa

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6i27

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 300000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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