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- EMDB-4806: CryoEM structure of Polytomella F-ATP synthase, focussed refineme... -

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Basic information

Entry
Database: EMDB / ID: EMD-4806
TitleCryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
Map data
Sample
  • Complex: Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
    • Protein or peptide: x 8 types
  • Ligand: x 4 types
Keywordsmitochondrial ATP synthase dimer flexible coupling cryoEM / PROTON TRANSPORT
Function / homology
Function and homology information


thylakoid / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / mitochondrion / membrane
Similarity search - Function
F1F0 ATP synthase subunit ASA5 / 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.
Similarity search - Domain/homology
Mitochondrial F1F0 ATP synthase associated 14 kDa protein / ASA-9: Polytomella F-ATP synthase associated subunit 9 / ASA-10: Polytomella F-ATP synthase associated subunit 10 / Mitochondrial ATP synthase subunit ASA6 / Mitochondrial ATP synthase subunit ASA8 / F-ATPase protein 6 / Mitochondrial F1F0 ATP synthase associated 32 kDa protein / ATP synthase associated protein ASA1
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsMurphy BJ / Klusch N
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Molecular Biology OrganizationALTF 702 2016 Germany
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-6rd5
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rd5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4806.png

Downloads & links

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Map

FileDownload / File: emd_4806.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-0.14779738 - 0.32990515
Average (Standard dev.)-0.000017805423 (±0.0053946623)
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-0.1480.330-0.000

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Supplemental data

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Half map: #1

Fileemd_4806_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_4806_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polytomella F-ATP synthase, focussed refinement of Fo and periphe...

EntireName: Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
Components
  • Complex: Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
    • Protein or peptide: ASA-10: Polytomella F-ATP synthase associated subunit 10
    • Protein or peptide: ATP synthase associated protein ASA1
    • Protein or peptide: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
    • Protein or peptide: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA6
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA8
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA9
    • Protein or peptide: Mitochondrial ATP synthase subunit 6
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Polytomella F-ATP synthase, focussed refinement of Fo and periphe...

SupramoleculeName: Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: Generated by focussed refinement of the Fo and peripheral stalk region, with C2 symmetry applied
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)

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Macromolecule #1: ASA-10: Polytomella F-ATP synthase associated subunit 10

MacromoleculeName: ASA-10: Polytomella F-ATP synthase associated subunit 10
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 8.731866 KDa
SequenceString:
MSYSAYFAKA GFQFPAGLSA LVAGIVALNV CTGRPTKGTK EISNAEYNAT PIGYLQSPDQ HPTAFPKVPG MKDVHGSPHH HH

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Macromolecule #2: ATP synthase associated protein ASA1

MacromoleculeName: ATP synthase associated protein ASA1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 68.679906 KDa
SequenceString: MMRAAQKAKQ ELPATVLTQT RSYLAPLRSD FTEEITAPKV ASASNLVNEW NNKKQATENL MKLLQAYKDI GDAKSEPLLK NHNPRTFED RDYPVPDFRT QNLKAGDVPK FFDTVISTRA SAAIASKDKF WAGRKTEAEA ASAKASAAFP RVAVPEWKKG K TVSIENLN ...String:
MMRAAQKAKQ ELPATVLTQT RSYLAPLRSD FTEEITAPKV ASASNLVNEW NNKKQATENL MKLLQAYKDI GDAKSEPLLK NHNPRTFED RDYPVPDFRT QNLKAGDVPK FFDTVISTRA SAAIASKDKF WAGRKTEAEA ASAKASAAFP RVAVPEWKKG K TVSIENLN TVTDKYAAAL VPKRKLALPV LPEGVKKAVE DFAASVGQAK NASEVSELLA KSLAEKAVVT EGGKVVEGFS YV SKAVAAK VIATRRAEVH ERLLKLWAKR LLVSPELAIV PLNEFDAQLA SKFEGISPKY QELLSAVAQG NKTFAQRLNS SPA FSSFLL KREKAESEVP PSELELEAAQ KAAELEDPEV ALRTLLGPQM EALGASDLLL SEQIRVITEH RYTPDRLQYK EGMK LADKI AAQEAALKEE LKVIYGDNVD VKHFQASPRT PVQQLFDSLK NAAANKERAA KEAAAAASPY LAYAVTKKQE VQADP SNIP FDEVLYPQLS EELLELELSD IREDEIALEK AEEEELWLLT LTQQFKHIQK HFGIDLPHSV VAHMDPLLIK KIDWET TNA LEDFDITLDD MGAEDAKEQW GAENLSHHFL PLIRYRRDLA RKNGDRYGPD LVNGN

UniProtKB: ATP synthase associated protein ASA1

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Macromolecule #3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein

MacromoleculeName: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 34.850363 KDa
SequenceString: MRQASRLALS IRQAGNVEAA SAVPAMTRQF SAPGSHEHHE TPLSKVMPTV VSIPRKVACL ALGATKKVVC GLASSGPSQN LVSTFANKV IVEENLVNVA EIDVPFWSYW LSSAGFTSKD AFVKFAEAVK PKVAALSTSD ITNLTVAFKR ANYYDKDLFT G IEANVSAN ...String:
MRQASRLALS IRQAGNVEAA SAVPAMTRQF SAPGSHEHHE TPLSKVMPTV VSIPRKVACL ALGATKKVVC GLASSGPSQN LVSTFANKV IVEENLVNVA EIDVPFWSYW LSSAGFTSKD AFVKFAEAVK PKVAALSTSD ITNLTVAFKR ANYYDKDLFT G IEANVSAN FTKFETEQLL QIVATFDAFN HSSVAFLDDV ADSITYCNHY LAPVRAGADE LATLLTYYAK NGHERADLLA TV ARGFSEV SLGKLSAAQR KDTVLSALKA FQTFGFYPES IEAVIGAALV SPAEYSAEEL KEVEAVKVAA ENALGGEFVL IQE GAHGH

UniProtKB: Mitochondrial F1F0 ATP synthase associated 32 kDa protein

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Macromolecule #4: Mitochondrial F1F0 ATP synthase associated 14 kDa protein

MacromoleculeName: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 14.004376 KDa
SequenceString:
MKLLPESLQQ EAATAAVVAS WVLWHLDTQL LPTIMREHKL HACWAAAAKR YNEKLFKLNP SYDRVLSLPA VSKNQVLENV FHTAPKAPV EHLEKMVSAN SKVYDALNLQ SKRVLIWQVK PALF

UniProtKB: Mitochondrial F1F0 ATP synthase associated 14 kDa protein

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Macromolecule #5: Mitochondrial ATP synthase subunit ASA6

MacromoleculeName: Mitochondrial ATP synthase subunit ASA6 / type: protein_or_peptide / ID: 5 / 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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Macromolecule #6: Mitochondrial ATP synthase subunit ASA8

MacromoleculeName: Mitochondrial ATP synthase subunit ASA8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 9.883389 KDa
SequenceString:
MVLGEVYLKD ILRTPPTGAI PANVPHPFQT SFYTYATKKL IPRHWYLLGG FTFTITLYGI LDGLRDSGKK KAYDEAIHAG KTPYTAGGH

UniProtKB: Mitochondrial ATP synthase subunit ASA8

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Macromolecule #7: Mitochondrial ATP synthase subunit ASA9

MacromoleculeName: Mitochondrial ATP synthase subunit ASA9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 11.001712 KDa
SequenceString:
MAVTSFLGKA FEKYFYDFSA YEQFGLNRFL SSKGQYVALR HVGFVMVGVN VLLAANFPFN PPFPTIGMCP AGWEGTWVCQ ADKAKALEM YKEWKKSN

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Macromolecule #8: Mitochondrial ATP synthase subunit 6

MacromoleculeName: Mitochondrial ATP synthase subunit 6 / type: protein_or_peptide / ID: 8 / 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 #9: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 9 / Number of copies: 11 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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Macromolecule #10: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 10 / Number of copies: 8 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 55 / 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: 3840 pixel / Digitization - Dimensions - Height: 3712 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 388670
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 / Protocol: OTHER
Output model

PDB-6rd5:
CryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry

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