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- EMDB-46787: Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1,... -

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Basic information

Entry
Database: EMDB / ID: EMD-46787
TitleTrypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1), right wing focused refinement map
Map dataRNA-editing catalytic complex 1 (RECC1), right wing focused refinement map
Sample
  • Complex: RECC1
KeywordsRNA editing / tRNA / OB-fold / mitochondria / RNA BINDING PROTEIN
Biological speciesTrypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsLiu YT / Jih J / Zhou ZH / Aphasizhev R
Funding support United States, China, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI152408 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI177658 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI113157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145249 United States
National Natural Science Foundation of China (NSFC)32570759 China
CitationJournal: To Be Published
Title: Structural basis of the mitochondrial RNA editing cascade in trypanosomes
Authors: Liu YT / Vacas AF / Jih J / Zhao X / Yu C / Lee JKJ / Suematsu T / Solayman M / Wang H / Wang X / Huang L / Zhang L / Aphasizheva I / Zhou ZH / Aphasizhev R
History
DepositionAug 28, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46787.png

Downloads & links

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Map

FileDownload / File: emd_46787.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA-editing catalytic complex 1 (RECC1), right wing focused refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.71033406 - 1.2369173
Average (Standard dev.)0.0008488558 (±0.020558294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: RNA-editing catalytic complex 1 (RECC1), right wing focused...

Fileemd_46787_half_map_1.map
AnnotationRNA-editing catalytic complex 1 (RECC1), right wing focused refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RNA-editing catalytic complex 1 (RECC1), right wing focused...

Fileemd_46787_half_map_2.map
AnnotationRNA-editing catalytic complex 1 (RECC1), right wing focused refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RECC1

EntireName: RECC1
Components
  • Complex: RECC1

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Supramolecule #1: RECC1

SupramoleculeName: RECC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17 / Details: From T. brucei mitochondrial T2 isolate
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Organelle: Mitochondria

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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: 7.6
Component:
ConcentrationFormulaName
60.0 mMKClPotassium chloride
25.0 mMTris-HClTris hydrochloride
10.0 mMMgCl2Magnesium chloride
5.0 mMOGn-Octylglucoside
1.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsFrom T. brucei mitochondrial T2 isolate

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 23092 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 40988 / Average exposure time: 3.5 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
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

Image recording ID2
DetailsFalcon 4i and K3 Bioquantum images were combined for processing.
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93504
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsConsensus map and focused refinement maps were combined to generate a composite map for final model refinement.
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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