[English] 日本語
Yorodumi
- EMDB-10857: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10857
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - Fo-wing region
Map dataLocal-resolution filtered full map of T. thermophila ATP synthase Fo-wing region
Sample
  • Complex: Mitochondrial ATP synthase, Fo-wing region
    • Protein or peptide: ATPTT1
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Keywordsmitochondria / ATP synthase / oxidoreductase / NAD / MEMBRANE PROTEIN
Function / homologySulphide quinone-reductase / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD binding / FAD/NAD(P)-binding domain superfamily / mitochondrion / Oxidoreductase, putative
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKock Flygaard R / Muhleip A
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts /
Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.
History
DepositionApr 14, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ynv
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ynv
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10857.png

Downloads & links

-
Map

FileDownload / File: emd_10857.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal-resolution filtered full map of T. thermophila ATP synthase Fo-wing region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.0507408 - 0.11670689
Average (Standard dev.)0.00030394032 (±0.0020931524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z498.000498.000498.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0510.1170.000

-
Supplemental data

-
Mask #1

Fileemd_10857_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_10857_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2

Fileemd_10857_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mitochondrial ATP synthase, Fo-wing region

EntireName: Mitochondrial ATP synthase, Fo-wing region
Components
  • Complex: Mitochondrial ATP synthase, Fo-wing region
    • Protein or peptide: ATPTT1
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

-
Supramolecule #1: Mitochondrial ATP synthase, Fo-wing region

SupramoleculeName: Mitochondrial ATP synthase, Fo-wing region / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

-
Macromolecule #1: ATPTT1

MacromoleculeName: ATPTT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 54.917816 KDa
SequenceString: MIHCLRNIRT VSALQSKISY NLGGGNKRKK TSGDLDNYDV LFVGANLGGI CSNHFDKDTH GKYKCFVSFD QPINQIYSVR IPYEQQRVR KSEYIHFSKK SINQFTPSEM LAVKEILPEQ NAVVLSSGRR IGYNQLVLAT GLKHDFSQIK GFYEALEHPE H PVYANRDP ...String:
MIHCLRNIRT VSALQSKISY NLGGGNKRKK TSGDLDNYDV LFVGANLGGI CSNHFDKDTH GKYKCFVSFD QPINQIYSVR IPYEQQRVR KSEYIHFSKK SINQFTPSEM LAVKEILPEQ NAVVLSSGRR IGYNQLVLAT GLKHDFSQIK GFYEALEHPE H PVYANRDP ETWRSAQHKY SKYISNFKSG DGYFCIPEYP YAGEVECFNF FVSDEVWKWA QHHGALSPKH TFTIVNANEK FV HYCDSAD AFIKERLEKR GIRVEYNTKL LEVHQDGQKA TFINTKTGEK SVRDYNNLYS IVPSKRQEFL DKAGLTNGNG LLN VDHQTL QHKKYKNIFG LGDAADLPTT KTFWAGWYQI AVVRNNVKRN LQGQTLNAHY DGFSKVPLFT GHQTLTYVAH SYGG VGNWQ HLKHNNGGIL AWMRYRSWAK GMAKKFQDFY NGARLGPPYH KVLKSFPELP GSPESQQSSG ISKYFPTKTE NKAAH

UniProtKB: Oxidoreductase, putative

-
Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: beta / Number images used: 61157
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: beta
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: beta
FSC plot (resolution estimation)

+
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