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- EMDB-11369: bovine ATP synthase monomer state 3 (combined) -

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Basic information

Entry
Database: EMDB / ID: EMD-11369
Titlebovine ATP synthase monomer state 3 (combined)
Map dataState 3 composite map created using PHENIX combinefocusedmaps
Sample
  • Complex: Bovine ATP synthase
    • Complex: monomeric bovine ATP synthase, state 3
      • Protein or peptide: x 17 types
    • Complex: Bovine ATP synthase
      • Protein or peptide: x 1 types
  • Ligand: x 6 types
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / proton-transporting ATP synthase complex ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / proton-transporting ATP synthase complex / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / mitochondrial membrane / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial ATPase inhibitor, IATP / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial ...ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase protein 8 / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase membrane subunit K, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Bovine (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSpikes TE / Montgomery MG / Walker JE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
History
DepositionJul 10, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.92
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.92
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zqn
  • Surface level: 7.92
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11369.png

Downloads & links

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Map

FileDownload / File: emd_11369.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState 3 composite map created using PHENIX combinefocusedmaps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 500 pix.
= 524. Å		1.05 Å/pix.
x 500 pix.
= 524. Å		1.05 Å/pix.
x 500 pix.
= 524. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.92 / Movie #1: 7.92
Minimum - Maximum-26.42356 - 45.02877
Average (Standard dev.)0.017483959 (±1.1030537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-26.42445.0290.017

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Supplemental data

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Sample components

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Entire : Bovine ATP synthase

EntireName: Bovine ATP synthase
Components
  • Complex: Bovine ATP synthase
    • Complex: monomeric bovine ATP synthase, state 3
      • Protein or peptide: ATP synthase subunit alpha, mitochondrial
      • Protein or peptide: ATP synthase subunit beta, mitochondrial
      • Protein or peptide: ATP synthase subunit gamma, mitochondrial
      • Protein or peptide: ATP synthase subunit delta, mitochondrial
      • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
      • Protein or peptide: ATP synthase F(0) complex subunit C2, mitochondrial
      • Protein or peptide: ATP synthase subunit O, mitochondrial
      • Protein or peptide: ATP synthase protein 8
      • Protein or peptide: ATP synthase subunit a
      • Protein or peptide: ATP synthase subunit d, mitochondrial
      • Protein or peptide: ATP synthase subunit f, mitochondrial
      • Protein or peptide: ATP synthase subunit g, mitochondrial
      • Protein or peptide: ATP synthase subunit ATP5MPL, mitochondrial
      • Protein or peptide: ATP synthase F(0) complex subunit B1, mitochondrial
      • Protein or peptide: ATP synthase-coupling factor 6, mitochondrial
      • Protein or peptide: ATP synthase membrane subunit DAPIT, mitochondrial
      • Protein or peptide: ATP synthase subunit e, mitochondrial
    • Complex: Bovine ATP synthase
      • Protein or peptide: ATPase inhibitor, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: water

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Supramolecule #1: Bovine ATP synthase

SupramoleculeName: Bovine ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18 / Details: bovine ATP synthase inhibited by IF1 1-60His
Molecular weightExperimental: 7.441 KDa

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Supramolecule #2: monomeric bovine ATP synthase, state 3

SupramoleculeName: monomeric bovine ATP synthase, state 3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#18
Details: monomeric bovine ATP synthase inhibited by IF1 1-60His, state 3
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Bovine ATP synthase

SupramoleculeName: Bovine ATP synthase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Bos taurus (domestic cattle)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 55.302191 KDa
SequenceString: EKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKARRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII ...String:
EKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKARRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII GDRQTGKTSI AIDTIINQKR FNDGTDEKKK LYCIYVAIGQ KRSTVAQLVK RLTDADAMKY TIVVSATASD AA PLQYLAP YSGCSMGEYF RDNGKHALII YDDLSKQAVA YRQMSLLLRR PPGREAYPGD VFYLHSRLLE RAAKMNDAFG GGS LTALPV IETQAGDVSA YIPTNVISIT DGQIFLETEL FYKGIRPAIN VGLSVSRVGS AAQTRAMKQV AGTMKLELAQ YREV AAFAQ FGSDLDAATQ QLLSRGVRLT ELLKQGQYSP MAIEEQVAVI YAGVRGYLDK LEPSKITKFE NAFLSHVISQ HQALL GKIR TDGKISEESD AKLKEIVTNF LAGFEA

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Macromolecule #2: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 51.757836 KDa
SequenceString: AAQASPSPKA GATTGRIVAV IGAVVDVQFD EGLPPILNAL EVQGRETRLV LEVAQHLGES TVRTIAMDGT EGLVRGQKVL DSGAPIRIP VGPETLGRIM NVIGEPIDER GPIKTKQFAA IHAEAPEFVE MSVEQEILVT GIKVVDLLAP YAKGGKIGLF G GAGVGKTV ...String:
AAQASPSPKA GATTGRIVAV IGAVVDVQFD EGLPPILNAL EVQGRETRLV LEVAQHLGES TVRTIAMDGT EGLVRGQKVL DSGAPIRIP VGPETLGRIM NVIGEPIDER GPIKTKQFAA IHAEAPEFVE MSVEQEILVT GIKVVDLLAP YAKGGKIGLF G GAGVGKTV LIMELINNVA KAHGGYSVFA GVGERTREGN DLYHEMIESG VINLKDATSK VALVYGQMNE PPGARARVAL TG LTVAEYF RDQEGQDVLL FIDNIFRFTQ AGSEVSALLG RIPSAVGYQP TLATDMGTMQ ERITTTKKGS ITSVQAIYVP ADD LTDPAP ATTFAHLDAT TVLSRAIAEL GIYPAVDPLD STSRIMDPNI VGSEHYDVAR GVQKILQDYK SLQDIIAILG MDEL SEEDK LTVSRARKIQ RFLSQPFQVA EVFTGHLGKL VPLKETIKGF QQILAGEYDH LPEQAFYMVG PIEEAVAKAD KLAEE HS

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Macromolecule #3: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 30.30076 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ISYKTEEKPI FSLDTISSAE SMSIYDDIDA DVLRNYQEYS LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD

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Macromolecule #4: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 15.074813 KDa
SequenceString:
AEAAAAQAPA AGPGQMSFTF ASPTQVFFNS ANVRQVDVPT QTGAFGILAA HVPTLQVLRP GLVVVHAEDG TTSKYFVSSG SVTVNADSS VQLLAEEAVT LDMLDLGAAK ANLEKAQSEL LGAADEATRA EIQIRIEANE ALVKALE

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Macromolecule #5: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 5.662693 KDa
SequenceString:
VAYWRQAGLS YIRYSQICAK AVRDALKTEF KANAMKTSGS TIKIVKVKKE

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Macromolecule #6: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 6
Details: ATP synthase inhibitor protein IF1 residues 1-60 with a 6His tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.462098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSESGDNVRS SAGAVRDAGG AFGKREQAEE ERYFRARAKE QLAALKKHHE NEISHHAKEI HHHHHH

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Macromolecule #7: ATP synthase F(0) complex subunit C2, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C2, mitochondrial / type: protein_or_peptide / ID: 7
Details: Residue 43 is trimethyllysine. A postranslational modification
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 7.653034 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SL(M3L)QQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

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Macromolecule #8: ATP synthase subunit O, mitochondrial

MacromoleculeName: ATP synthase subunit O, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 20.959777 KDa
SequenceString:
FAKLVRPPVQ IYGIEGRYAT ALYSAASKQN KLEQVEKELL RVGQILKEPK MAASLLNPYV KRSVKVKSLS DMTAKEKFSP LTSNLINLL AENGRLTNTP AVISAFSTMM SVHRGEVPCT VTTASALDEA TLTELKTVLK SFLSKGQVLK LEVKIDPSIM G GMIVRIGE KYVDMSAKTK IQKLSRAMRE IL

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Macromolecule #9: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 7.944523 KDa
SequenceString:
MPQLDTSTWL TMILSMFLTL FIIFQLKVSK HNFYHNPELT PTKMLKQNTP WETKWTKIYL PLLLPL

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Macromolecule #10: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 24.801785 KDa
SequenceString: MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH ...String:
MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH LLIHLIGGAT LALMSISTTT ALITFTILIL LTILEFAVAM IQAYVFTLLV SLYLHDNT

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Macromolecule #11: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 18.588256 KDa
SequenceString:
AGRKLALKTI DWVAFGEIIP RNQKAVANSL KSWNETLTSR LATLPEKPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPI PEDKYTAQV DAEEKEDVKS CAEFLTQSKT RIQEYEKELE KMRNIIPFDQ MTIEDLNEVF PETKLDKKKY PYWPHRPIET L

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Macromolecule #12: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 10.184011 KDa
SequenceString:
ASVVPLKEKK LLEVKLGELP SWILMRDFTP SGIAGAFQRG YYRYYNKYVN VKKGSIAGLS MVLAAYVFLN YCRSYKELKH ERLRKYH

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Macromolecule #13: ATP synthase subunit g, mitochondrial

MacromoleculeName: ATP synthase subunit g, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 11.298196 KDa
SequenceString:
AEFVRNLAEK APALVNAAVT YSKPRLATFW YYAKVELVPP TPAEIPTAIQ SLKKIINSAK TGSFKQLTVK EALLNGLVAT EVWMWFYVG EIIGKRGIIG YDV

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Macromolecule #14: ATP synthase subunit ATP5MPL, mitochondrial

MacromoleculeName: ATP synthase subunit ATP5MPL, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 6.846093 KDa
SequenceString:
MLQSLIKKVW IPMKPYYTQA YQEIWVGTGL MAYIVYKIRS ADKRSKALKA SSAAPAHGHH

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Macromolecule #15: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 24.702709 KDa
SequenceString: PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK ...String:
PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK EQEHMINWVE KRVVQSISAQ QEKETIAKCI ADLKLLSKKA QAQPVM

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Macromolecule #16: ATP synthase-coupling factor 6, mitochondrial

MacromoleculeName: ATP synthase-coupling factor 6, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 8.971079 KDa
SequenceString:
NKELDPVQKL FVDKIREYRT KRQTSGGPVD AGPEYQQDLD RELFKLKQMY GKADMNTFPN FTFEDPKFEV VEKPQS

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Macromolecule #17: ATP synthase membrane subunit DAPIT, mitochondrial

MacromoleculeName: ATP synthase membrane subunit DAPIT, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 6.312383 KDa
SequenceString:
AGPEADAQFH FTGIKKYFNS YTLTGRMNCV LATYGSIALI VLYFKLRSKK TPAVKAT

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Macromolecule #18: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 8.205492 KDa
SequenceString:
VPPVQVSPLI KLGRYSALFL GMAYGAKRYN YLKPRAEEER RLAAEEKKKR DEQKRIEREL AEAQEDTILK

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Macromolecule #19: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #21: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 21 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #22: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 22 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 17 / 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

Concentration4.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV
Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting..
DetailsNickel affinity purified filled by gel filtration

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 4.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

CTF correctionSoftware: (Name: RELION (ver. 3.1), CTFFIND (ver. 4.1))
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2v7q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 61458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial model
PDB IDChain

2v7q

chain_id: A

2v7q

chain_id: B

2v7q

chain_id: C

2v7q

chain_id: D

2v7q

chain_id: E

2v7q

chain_id: F

2v7q

chain_id: G

2v7q

chain_id: H

2v7q

chain_id: I

2v7q

chain_id: J

2cly

chain_id: A

2cly

chain_id: B

2cly

chain_id: C
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6zqn:
bovine ATP synthase monomer state 3 (combined)

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