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- EMDB-4807: CryoEM structure of Polytomella F-ATP synthase, focussed refineme... -

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Basic information

Entry
Database: EMDB / ID: EMD-4807
TitleCryoEM structure of Polytomella F-ATP synthase, focussed refinement of upper peripheral stalk
Map data
Sample
  • Complex: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pringsheim 198.80
    • Protein or peptide: ASA-2: Polytomella F-ATP synthase associated subunit 2
    • Protein or peptide: Mitochondrial ATP synthase associated protein ASA4
    • Protein or peptide: Mitochondrial ATP synthase associated protein ASA7
    • Protein or peptide: Mitochondrial ATP synthase subunit OSCP
    • Protein or peptide: ATP synthase subunit alpha
  • Ligand: water
Keywordsmitochondrial ATP synthase dimer flexible coupling cryoEM / PROTON TRANSPORT
Function / homology
Function and homology information


: / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / hydrolase activity / ATP binding / membrane
Similarity search - Function
ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain ...ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit alpha / Mitochondrial ATP synthase associated protein ASA4 / Mitochondrial ATP synthase subunit ASA2 / Mitochondrial ATP synthase subunit OSCP / Mitochondrial ATP synthase associated protein ASA7
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMurphy BJ / Klusch N
Funding supporttopol, European Molecular Biology Organization, 2 items
OrganizationGrant numberCountry
Max Planck SocietyGermanytopol
1GermanyEuropean Molecular Biology Organization
CitationJournal: Science / Year: 2019
Title: Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling.
Authors: Bonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy ...FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany -ring rotation and result in ATP synthesis. Crucially, the F head rotates along with the central stalk and -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F and F subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize -ring protonation with rotation.
History
DepositionApr 12, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rd6
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rd6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4807.png

Downloads & links

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Map

FileDownload / File: emd_4807.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.)
1.05 Å/pix.
x 480 pix.
= 505.44 Å		1.05 Å/pix.
x 480 pix.
= 505.44 Å		1.05 Å/pix.
x 480 pix.
= 505.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.17543729 - 0.3147185
Average (Standard dev.)-0.000023048033 (±0.004600306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 505.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z505.440505.440505.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1750.315-0.000

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Supplemental data

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Half map: #1

Fileemd_4807_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4807_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pr...

EntireName: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pringsheim 198.80
Components
  • Complex: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pringsheim 198.80
    • Protein or peptide: ASA-2: Polytomella F-ATP synthase associated subunit 2
    • Protein or peptide: Mitochondrial ATP synthase associated protein ASA4
    • Protein or peptide: Mitochondrial ATP synthase associated protein ASA7
    • Protein or peptide: Mitochondrial ATP synthase subunit OSCP
    • Protein or peptide: ATP synthase subunit alpha
  • Ligand: water

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Supramolecule #1: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pr...

SupramoleculeName: Dimeric mitochondrial F-type ATP synthase from Polytomella sp. Pringsheim 198.80
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Generated using a symmetry-expanded dataset, with focussed refinement of the upper peripheral stalk region of one monomer
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)

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Macromolecule #1: ASA-2: Polytomella F-ATP synthase associated subunit 2

MacromoleculeName: ASA-2: Polytomella F-ATP synthase associated subunit 2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 44.842121 KDa
SequenceString: ENDVPAILKE IDSLVSREAV SAKEVSDAAV ALTYLQVKAN RRLWGKVLEK AGAAQDYDAA SLTNLLWAIN TGGVEHFKTV AELAGPAVS LLPSLSPVQL SIVVEALGGA GVKNYELYNK ASAVVVSKIG EFKPAEIARV LYGVAFGGVN DVALAKAAGK V FASTEVDS ...String:
ENDVPAILKE IDSLVSREAV SAKEVSDAAV ALTYLQVKAN RRLWGKVLEK AGAAQDYDAA SLTNLLWAIN TGGVEHFKTV AELAGPAVS LLPSLSPVQL SIVVEALGGA GVKNYELYNK ASAVVVSKIG EFKPAEIARV LYGVAFGGVN DVALAKAAGK V FASTEVDS RTAAQALYAL AKLGRADKAT VDALLKSFKK GTESASDAAA ASFALGSLSF KAEKAIVDAL KASAGDLAPA QA VEAAYGL ALSGATDAEA FKALFGVVAP AIEKAPDALE VSSLAQLHVA STISGAKLPA AVGSFVAKAF GLAADAARLK RSS AESALV ADVAAATAVA FGAQYRPEVA SAVASYVKTA PDGSVLDIAI TKGDAKVLVQ AVPSSLLTST TPAKPLGHVA AYSK VREAQ GYAVAVVPAN EFEALPDQKA KAQYVLAAIK KVAPSF

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Macromolecule #2: Mitochondrial ATP synthase associated protein ASA4

MacromoleculeName: Mitochondrial ATP synthase associated protein ASA4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 31.275113 KDa
SequenceString: ATEPAVSKKE VLYFLSSKDA ESSTAVKSYL KSLYAGAQVE ATETDASELI AQLEKKYLSA QVVEPGVHNI ALPLGESGSA PVKRYAAEL FNLGAQAGFE CPFIEVSKKF GQETATSETV KDVLNKTKSY VSADYNAALN EVLSSVEAEI NGPVLFDGKT E GFKKFAAK ...String:
ATEPAVSKKE VLYFLSSKDA ESSTAVKSYL KSLYAGAQVE ATETDASELI AQLEKKYLSA QVVEPGVHNI ALPLGESGSA PVKRYAAEL FNLGAQAGFE CPFIEVSKKF GQETATSETV KDVLNKTKSY VSADYNAALN EVLSSVEAEI NGPVLFDGKT E GFKKFAAK AKAVAVSRGL PADTILAYCA GSANEDAADK VSKEFFTWFE SAYTADAAAE VKAIEAEAAS ILDRHLAKPV AQ IRKEQAS AYASLLKRAE TAKGAKWAEK YLEDVKAVQW FDASVAEAPA SGPKVAA

UniProtKB: Mitochondrial ATP synthase associated protein ASA4

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Macromolecule #3: Mitochondrial ATP synthase associated protein ASA7

MacromoleculeName: Mitochondrial ATP synthase associated protein ASA7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 20.55316 KDa
SequenceString:
MSSVRAGVEA GRRDLTTFTF SGLQDAPVAA LSGSIKLNVA AKAGKAEVTV AAGAAKAATQ VSAAALRKLS GSKISLAEVA RISVLHSSI QNYLLSLSNE RYQLLSQWPD FTTMYGKDFY YRAHPEDLKK FYDAADEYYK LYETVTEFDS LSALASQVVP N YAARRRST VHPAIGSTVA DGAFTNFLLS KQ

UniProtKB: Mitochondrial ATP synthase associated protein ASA7

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Macromolecule #4: Mitochondrial ATP synthase subunit OSCP

MacromoleculeName: Mitochondrial ATP synthase subunit OSCP / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 25.530793 KDa
SequenceString: MLARVASVAL RRAEGKIMPQ MVRALSVSAA SAAQAELKLP TAPLQLSGTS AQIATLLWQV AAKENQLDKV QDELYQFIEL FKQHSELRR LATDPFVPTL VRTKIISSVL KDSGASEITK KLFEALADEG ALSALLEVTV NYEELMLAHK KEVYCTVITA E PLDKLERV ...String:
MLARVASVAL RRAEGKIMPQ MVRALSVSAA SAAQAELKLP TAPLQLSGTS AQIATLLWQV AAKENQLDKV QDELYQFIEL FKQHSELRR LATDPFVPTL VRTKIISSVL KDSGASEITK KLFEALADEG ALSALLEVTV NYEELMLAHK KEVYCTVITA E PLDKLERV ELTKKAEKFV DAGFKLVMQE KIDKKLLGGF VIEFSDRRVD MSTAKKVEEF NNFVNKLVLS I

UniProtKB: Mitochondrial ATP synthase subunit OSCP

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Macromolecule #5: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 60.766152 KDa
SequenceString: MRSPAAFVAR SGLFKASLGQ SNWAQKAEQM MASVTRTFAA DAKALDELRK PKFSSKYLIQ HVSQKLIPAV KEWEKSYQPP VIHLGRVLS VGDGIARVYG LKSVQAGELV CFDSGVKGMA LNLQADHVGV VVFGNDSVIH QGDLVYRTGQ IVNVPIGPGT L GRVTDGLG ...String:
MRSPAAFVAR SGLFKASLGQ SNWAQKAEQM MASVTRTFAA DAKALDELRK PKFSSKYLIQ HVSQKLIPAV KEWEKSYQPP VIHLGRVLS VGDGIARVYG LKSVQAGELV CFDSGVKGMA LNLQADHVGV VVFGNDSVIH QGDLVYRTGQ IVNVPIGPGT L GRVTDGLG QPIDGKGPLT NVRSSLVEVK APGIIARQSV REPLFTGVKA VDALVPIGRG QRELIIGDRQ TGKTAVAIDA II HQKNCNE QVPKAQRVYC VYVAVGQKRS TVAQLVKLFT QTGAMRYTIM VSATASDAAP LQFLAPYSGC AMAEYFRDTG KHG LIIYDD LSKQSVAYRQ MSLLLRRPPG REAFPGDVFY LHSRLLERAA KLSKELGGGS LTAFPVIETQ AGDVSAYIAT NVIS ITDGQ IFLETELFYK GIRPALNVGL SVSRVGSAAQ FPGMKQVAGT LKLELAQYRE VAAFAQFGSD LDAATQYVLE RGARL TEML KQKQFAPIPI ERQTVAVYAA TKGFLDKVRV QDIVAAEEAV ISQVNPAVFK ILKANGKITP ALDAHLKAEL RKVKLP GA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -5.0 µm / Nominal defocus min: -0.4 µm / Nominal magnification: 75000
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: 735197
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 777340
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6rd6:
CryoEM structure of Polytomella F-ATP synthase, focussed refinement of upper peripheral stalk

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