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- EMDB-52062: Translation-initiation state of human mitochondrial ribosome smal... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52062
TitleTranslation-initiation state of human mitochondrial ribosome small subunit (State D)
Map dataBody-focused map of state D
Sample
  • Complex: Translation-initiation state of human mitochondrial ribosome small subunit (State D)
Keywordsmitochondrial ribosomal small subunit / translation-initiation intermediate / immature h44 / single-particle cryo-EM / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFinke AF / Heinrichs M / Aibara S / Richter-Dennerlein R / Hillen HS
Funding support Germany, European Union, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)RI 2715/1- 1 Germany
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB1190 Germany
German Research Foundation (DFG)SFB1565 Germany
European Research Council (ERC)101116869European Union
CitationJournal: Nat Commun / Year: 2025
Title: Coupling of ribosome biogenesis and translation initiation in human mitochondria
Authors: Heinrichs M / Finke AF / Aibara S / Hillen HS / Richter-Dennerlein R
History
DepositionNov 12, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52062.png

Downloads & links

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Map

FileDownload / File: emd_52062.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody-focused map of state D
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.467
Minimum - Maximum-1.8629838 - 4.160078
Average (Standard dev.)0.0006244574 (±0.0928583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 461.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52062_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of body-focused map of state D

Fileemd_52062_half_map_1.map
AnnotationHalf-map 2 of body-focused map of state D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of body-focused map of state D

Fileemd_52062_half_map_2.map
AnnotationHalf-map 1 of body-focused map of state D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Translation-initiation state of human mitochondrial ribosome smal...

EntireName: Translation-initiation state of human mitochondrial ribosome small subunit (State D)
Components
  • Complex: Translation-initiation state of human mitochondrial ribosome small subunit (State D)

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Supramolecule #1: Translation-initiation state of human mitochondrial ribosome smal...

SupramoleculeName: Translation-initiation state of human mitochondrial ribosome small subunit (State D)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Details: Translation-initiation mtSSU intermediate with immature h44 and in complex with mtIF3.
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293T
Molecular weightTheoretical: 990 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

BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHepes-HCl
100.0 mMPotassium chlorideKCl
20.0 mMMagnesium chlorideMgCl2
0.02 %DDM
1.0 mMPMSF
1.0 Xprotease-inhibitor mix
0.5 mMGMP-PNP

Details: 20mM HEPES-HCl, 100mM KCl, 20mM MgCl2, 0.02% DDM, 1mM PMSF, 1x protease-inhibitor mix, 0.5mM GMP-PNP
GridModel: Quantifoil R3.5/1 / Material: COPPER / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: The grid was precoated with a 2-3 nm carbon layer.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was crosslinked with 0.15% glutaraldehyde for 10 min on ice. The reaction was stopped by adding 50 mM lysine pH 7.5 and 50 mM aspartate pH 7.5, and subsequently desalted against the final buffer prior to vitrification.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 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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Image processing

Particle selectionNumber selected: 5730547
Startup modelType of model: NONE / Details: ab initio reconstruction after 2D classification
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1.) / Number images used: 80262
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 109367 / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

Initial model
PDB IDChain

7po1

chain_id: A, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: B, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: C, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: D, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: E, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: F, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: G, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: H, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: I, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: J, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: K, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: L, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: M, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: N, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: O, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: P, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: Q, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: R, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: S, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: T, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: U, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: V, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: W, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: X, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: Y, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: Z, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: 0, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: 1, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: 2, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: 3, source_name: PDB, initial_model_type: experimental model

7po1

chain_id: 4, source_name: PDB, initial_model_type: experimental model

7po2

chain_id: 8, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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