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- EMDB-4176: Polytomella Fo model -

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Basic information

Entry
Database: EMDB / ID: EMD-4176
TitlePolytomella Fo model
Map data
Sample
  • Complex: Polytommella mitochondrial ATP synthase Fo complex
    • Protein or peptide: Mitochondrial ATP synthase subunit c
    • Protein or peptide: Mitochondrial ATP synthase subunit 6
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA6
Keywordselectron cryo-microscopy mitochondrial ATP synthase membrane protein energy conversion proton pathway / PROTON TRANSPORT
Function / homology
Function and homology information


proton transmembrane transporter activity / proton motive force-driven ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / lipid binding
Similarity search - Function
ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. ...ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
Mitochondrial ATP synthase subunit c / Mitochondrial ATP synthase subunit ASA6 / F-ATPase protein 6
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYildiz O / Kuehlbrandt W
Funding support Germany, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research FoundationSFB807 Germany
European Molecular Biology Organization Germany
CitationJournal: Elife / Year: 2017
Title: Structural basis of proton translocation and force generation in mitochondrial ATP synthase.
Authors: Niklas Klusch / Bonnie J Murphy / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton ...ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton pathway. We determined the structure of an intact mitochondrial ATP synthase dimer by electron cryo-microscopy at near-atomic resolution. Charged and polar residues of the -subunit stator define two aqueous channels, each spanning one half of the membrane. Passing through a conserved membrane-intrinsic helix hairpin, the lumenal channel protonates an acidic glutamate in the -ring rotor. Upon ring rotation, the protonated glutamate encounters the matrix channel and deprotonates. An arginine between the two channels prevents proton leakage. The steep potential gradient over the sub-nm inter-channel distance exerts a force on the deprotonated glutamate, resulting in net directional rotation.
History
DepositionNov 28, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f36
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f36
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4176.png

Downloads & links

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Map

FileDownload / File: emd_4176.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 480 pix.
= 530.4 Å		1.11 Å/pix.
x 480 pix.
= 530.4 Å		1.11 Å/pix.
x 480 pix.
= 530.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.088374175 - 0.14797704
Average (Standard dev.)0.000022298946 (±0.0010020757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 530.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1051.1051.105
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z530.400530.400530.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0880.1480.000

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Supplemental data

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Sample components

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Entire : Polytommella mitochondrial ATP synthase Fo complex

EntireName: Polytommella mitochondrial ATP synthase Fo complex
Components
  • Complex: Polytommella mitochondrial ATP synthase Fo complex
    • Protein or peptide: Mitochondrial ATP synthase subunit c
    • Protein or peptide: Mitochondrial ATP synthase subunit 6
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA6

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Supramolecule #1: Polytommella mitochondrial ATP synthase Fo complex

SupramoleculeName: Polytommella mitochondrial ATP synthase Fo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Mitochondrial ATP synthase subunit c

MacromoleculeName: Mitochondrial ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 12.664013 KDa
SequenceString:
MSVQRLSLGA ARCLSAGVAR VQASQALVAQ KAVAVAPTRA QAAPAEVAQV RSMSVLAASK MVGAGCATIA LAGVGAGLGV MFGSLINGA ARNPNIAKQL VGYALLGFAL TESIALFSLL VVFLILFA

UniProtKB: Mitochondrial ATP synthase subunit c

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Macromolecule #2: Mitochondrial ATP synthase subunit 6

MacromoleculeName: Mitochondrial ATP synthase subunit 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 34.802344 KDa
SequenceString: MSVLSSVSMG SRIGSSLLGR SSAYLAQCGF STRSNLNGSI DTSSSVFQAL SSDNENKPAA SPLNVKLPGM SCSSILLPKT SRIAVPFGN QTMAMSSVRD VKTGSLPTNF LTGVYRFWRS QNPAEKPHDP VNDRLLPAVV DASDKRASIG TWATTFFCTI I SCNLLGLM ...String:
MSVLSSVSMG SRIGSSLLGR SSAYLAQCGF STRSNLNGSI DTSSSVFQAL SSDNENKPAA SPLNVKLPGM SCSSILLPKT SRIAVPFGN QTMAMSSVRD VKTGSLPTNF LTGVYRFWRS QNPAEKPHDP VNDRLLPAVV DASDKRASIG TWATTFFCTI I SCNLLGLM PFNEAPTSGL GFATGLGVSV WATATILGLS KTGFKFPGHF IPGGTPWPMA FIFVPLETIS YTFRAVSLGV RL WVNMLAG HTLLHILTGM ALALPFSLGF FSMVPATFGV CCLLSALVGL EYLVAVLQSG VFSILSTVYV GEFNHDKFIG PAA KIVKKI H

UniProtKB: F-ATPase protein 6

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Macromolecule #3: Mitochondrial ATP synthase subunit ASA6

MacromoleculeName: Mitochondrial ATP synthase subunit ASA6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 15.90429 KDa
SequenceString:
MMLRTLTRSS AVAGQAVRLF KTSAAAAEGN SVAGIIKSVN ETSGANLLSS LKTIKAQAAP IYPAAASSTG YSTQAKIALF GALSWILYR ADGQSKAHEW IVDLNLNVLQ AAWLISFSSL IPFRAVYFAF RGMAPATAST LNGLKTFSSI SL

UniProtKB: Mitochondrial ATP synthase subunit ASA6

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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: 8
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-45 / Number grids imaged: 30 / Average exposure time: 0.2 sec. / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 4 / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90142
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6f36:
Polytomella Fo model

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