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- EMDB-19999: In situ structure of the peripheral stalk of the mitochondrial AT... -

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Basic information

Entry
Database: EMDB / ID: EMD-19999
TitleIn situ structure of the peripheral stalk of the mitochondrial ATPsynthase in whole Polytomella cells
Map dataPrimary map generated by PHENIX's density modification job.
Sample
  • Cell: Polytomella sp.
    • 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 associated protein ASA7
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA8
    • Protein or peptide: ASA-9: Polytomella F-ATP synthase associated subunit 9
    • Protein or peptide: Mitochondrial ATP synthase subunit 6
KeywordsATP synthesis / in situ / OXPHOS / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / proton-transporting ATP synthase activity, rotational mechanism / 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 associated protein ASA7 / 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 (plant) / Polytomella sp. Pringsheim 198.80 (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 5.6 Å
AuthorsDietrich L / Agip ANA / Kuehlbrandt W
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)FOR2848 Germany
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionMar 29, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19999.png

Downloads & links

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Map

FileDownload / File: emd_19999.map.gz / Format: CCP4 / Size: 19.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map generated by PHENIX's density modification job.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.63 Å/pix.
x 170 pix.
= 277.1 Å		1.63 Å/pix.
x 151 pix.
= 246.13 Å		1.63 Å/pix.
x 195 pix.
= 317.85 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0894
Minimum - Maximum-0.44851556 - 0.64719725
Average (Standard dev.)0.000000000000064 (±0.028615765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin155123145
Dimensions151195170
Spacing170151195
CellA: 277.1 Å / B: 246.13 Å / C: 317.85 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Polytomella sp.

EntireName: Polytomella sp.
Components
  • Cell: Polytomella sp.
    • 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 associated protein ASA7
    • Protein or peptide: Mitochondrial ATP synthase subunit ASA8
    • Protein or peptide: ASA-9: Polytomella F-ATP synthase associated subunit 9
    • Protein or peptide: Mitochondrial ATP synthase subunit 6

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Supramolecule #1: Polytomella sp.

SupramoleculeName: Polytomella sp. / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Polytomella (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

UniProtKB: ASA-10: Polytomella F-ATP synthase associated subunit 10

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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 associated protein ASA7

MacromoleculeName: Mitochondrial ATP synthase associated protein ASA7 / type: protein_or_peptide / ID: 6 / 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 #7: Mitochondrial ATP synthase subunit ASA8

MacromoleculeName: Mitochondrial ATP synthase subunit ASA8 / type: protein_or_peptide / ID: 7 / 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 #8: ASA-9: Polytomella F-ATP synthase associated subunit 9

MacromoleculeName: ASA-9: Polytomella F-ATP synthase associated subunit 9
type: protein_or_peptide / ID: 8 / 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

UniProtKB: ASA-9: Polytomella F-ATP synthase associated subunit 9

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Macromolecule #9: Mitochondrial ATP synthase subunit 6

MacromoleculeName: Mitochondrial ATP synthase subunit 6 / type: protein_or_peptide / ID: 9 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: GP2.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4040 pixel / Average electron dose: 1.9 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 / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 53000
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

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number subtomograms used: 238622
ExtractionNumber tomograms: 255 / Number images used: 363061 / Software - Name: STOPGAP
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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