[English] 日本語
Yorodumi
- EMDB-51058: Assembly intermediate of human mitochondrial ribosome small subun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51058
TitleAssembly intermediate of human mitochondrial ribosome small subunit (State C)
Map dataBody-focused map of state C
Sample
  • Complex: Assembly intermediate of human mitochondrial ribosome small subunit (State C)
Keywordsmitochondrial ribosomal small subunit / assembly 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
DepositionJul 15, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51058.png

Downloads & links

-
Map

FileDownload / File: emd_51058.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody-focused map of state C
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: 0.39
Minimum - Maximum-0.7272678 - 2.0289598
Average (Standard dev.)0.0005030268 (±0.051537707)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_51058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_51058_half_map_1.map
AnnotationHalf-map 2 of body-focused map of state C
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_51058_half_map_2.map
AnnotationHalf-map 1 of body-focused map of state C
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Assembly intermediate of human mitochondrial ribosome small subun...

EntireName: Assembly intermediate of human mitochondrial ribosome small subunit (State C)
Components
  • Complex: Assembly intermediate of human mitochondrial ribosome small subunit (State C)

-
Supramolecule #1: Assembly intermediate of human mitochondrial ribosome small subun...

SupramoleculeName: Assembly intermediate of human mitochondrial ribosome small subunit (State C)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Details: Early assembly mtSSU intermediate in complex with METTL15, and mtRBFA(out), and missing mS37, with immature h44 and partially h24.
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293T
Molecular weightTheoretical: 990 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
Electron microscopy

MicroscopeFEI TITAN 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

+
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: 79037
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: 8 / Avg.num./class: 77919 / Software - Name: RELION (ver. 3.0)

-
Atomic model buiding 1

Initial model
PDB IDChain

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

7pnx

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more