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- EMDB-71580: Porcine ATP synthase with inhibitory protein IF1, DP-state -

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Basic information

Entry
Database: EMDB / ID: EMD-71580
TitlePorcine ATP synthase with inhibitory protein IF1, DP-state
Map dataATP synthase with inhibitory protein IF1, DP-state
Sample
  • Complex: Mitochondrial ATP synthase
    • Protein or peptide: x 16 types
  • Ligand: x 3 types
KeywordsATP synthesis / Complex V / mitochondria / oxidative-phosphorylation / MEMBRANE PROTEIN / TRANSLOCASE
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex binding / : / : / mitochondrial depolarization / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATP biosynthetic process / positive regulation of type 2 mitophagy ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex binding / : / : / mitochondrial depolarization / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATP biosynthetic process / positive regulation of type 2 mitophagy / ATPase inhibitor activity / Mitochondrial translation termination / Mitochondrial protein degradation / proton channel activity / negative regulation of hydrolase activity / negative regulation of endothelial cell proliferation / heme biosynthetic process / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / negative regulation of cardiac muscle cell apoptotic process / response to ischemia / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / erythrocyte differentiation / ADP binding / mitochondrial membrane / ATPase binding / calmodulin binding / mitochondrial inner membrane / lipid binding / cell surface / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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 F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f ...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 F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 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, 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 delta/epsilon subunit, C-terminal domain superfamily / 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, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 / ATP synthase subunit b / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit epsilon / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATPase inhibitor, mitochondrial ...ATP synthase subunit beta / ATP synthase subunit b / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit epsilon / ATP synthase subunit gamma / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(0) complex subunit a / ATP synthase lipid-binding protein / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsMnatsakanyan N / Mello JFR / Palles C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG072484 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS137275 United States
CitationJournal: To Be Published
Title: Porcine ATP synthase with inhibitory protein IF1, DP-state
Authors: Mnatsakanyan N / Mello JFR / Palles C
History
DepositionJul 2, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_71580.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATP synthase with inhibitory protein IF1, DP-state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 512 pix.
= 546.816 Å
1.07 Å/pix.
x 512 pix.
= 546.816 Å
1.07 Å/pix.
x 512 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy EMDB: 5.1
Minimum - Maximum-24.262153999999999 - 51.984454999999997
Average (Standard dev.)0.012466257 (±1.0761626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ATP synthase with inhibitory protein IF1, DP-state

Fileemd_71580_half_map_1.map
AnnotationATP synthase with inhibitory protein IF1, DP-state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: ATP synthase with inhibitory protein IF1, DP-state

Fileemd_71580_half_map_2.map
AnnotationATP synthase with inhibitory protein IF1, DP-state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Mitochondrial ATP synthase

EntireName: Mitochondrial ATP synthase
Components
  • Complex: Mitochondrial ATP synthase
    • Protein or peptide: ATP synthase lipid-binding protein
    • Protein or peptide: ATP synthase F(1) complex subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase F(1) complex subunit delta, mitochondrial
    • Protein or peptide: ATP synthase F1 subunit epsilon
    • Protein or peptide: ATPase inhibitor, mitochondrial
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase peripheral stalk subunit F6, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase peripheral stalk subunit OSCP, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit 8
    • Protein or peptide: ATP synthase F(0) complex subunit f, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit g, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit e, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mitochondrial ATP synthase

SupramoleculeName: Mitochondrial ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: ATP synthase lipid-binding protein

MacromoleculeName: ATP synthase lipid-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.426718 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SMIIGYARNP SLKQQLFSYA ILGFALSEAM GLFCLMVAFL ILF

UniProtKB: ATP synthase lipid-binding protein

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Macromolecule #2: ATP synthase F(1) complex subunit alpha, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit alpha, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 55.100027 KDa
SequenceString: KTGTAEVSSI LEERILGADT SVDLEETGRV LSIGDGIARV HGLRNVQAEE MVEFSSGLKG MSLNLEPDNV GVVVFGNDKL IKEGDIVKR TGAIVDVPVG EELLGRVVDA LGNAIDGKGP IGSKTRRRVG LKAPGIIPRI SVREPMQTGI KAVDSLVPIG R GQRELIIG ...String:
KTGTAEVSSI LEERILGADT SVDLEETGRV LSIGDGIARV HGLRNVQAEE MVEFSSGLKG MSLNLEPDNV GVVVFGNDKL IKEGDIVKR TGAIVDVPVG EELLGRVVDA LGNAIDGKGP IGSKTRRRVG LKAPGIIPRI SVREPMQTGI KAVDSLVPIG R GQRELIIG DRQTGKTSIA IDTIINQKRF NDGTDEKKKL YCIYVAIGQK RSTVAQLVKR LTDADAMKYT IVVSATASDA AP LQYLAPY SGCSMGEYFR DNGKHALIIY DDLSKQAVAY RQMSLLLRRP PGREAYPGDV FYLHSRLLER AAKMNDAFGG GSL TALPVI ETQAGDVSAY IPTNVISITD GQIFLETELF YKGIRPAINV GLSVSRVGSA AQTRAMKQVA GTMKLELAQY REVA AFAQF GSDLDAATQQ LLSRGVRLTE LLKQGQYAPM AIEEQVAVIY AGVRGYLDKL EPSKITKFEN AFLSHVISQH QALLG KIRA DGKISEETDA KLKEIVTNFL AGFE

UniProtKB: ATP synthase F(1) complex subunit alpha, mitochondrial

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Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.67773 KDa
SequenceString: AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPVG PETLGRIMN VIGEPIDERG PIKTKQFAAI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG GAGVGKTVLI M ELINNVAK ...String:
AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPVG PETLGRIMN VIGEPIDERG PIKTKQFAAI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG GAGVGKTVLI M ELINNVAK AHGGYSVFAG VGERTREGND LYHEMIESGV INLKDATSKV ALVYGQMNEP PGARARVALT GLTVAEYFRD QE GQDVLLF IDNIFRFTQA GSEVSALLGR IPSAVGYQPT LATDMGTMQE RITTTKKGSI TSVQAIYVPA DDLTDPAPAT TFA HLDATT VLSRAIAELG IYPAVDPLDS TSRIMDPNIV GSEHYDVARG VQKILQDYKS LQDIIAILGM DELSEEDKLT VSRA RKIQR FLSQPFQVAE VFTGHLGKLV PLKETIKGFQ QILAGEYDHL PEQAFYMVGP IEEAVAKADK LAEEH

UniProtKB: ATP synthase subunit beta

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Macromolecule #4: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 30.12165 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERDLKP ARVYGIGSLA LYEKADIKVP EDKKKHLIIG VSSDRGLCGA IHSSVAKQI KSEVANLTAA GKEVKIVGVG DKIRGILHRT HSDQFLVTFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERDLKP ARVYGIGSLA LYEKADIKVP EDKKKHLIIG VSSDRGLCGA IHSSVAKQI KSEVANLTAA GKEVKIVGVG DKIRGILHRT HSDQFLVTFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ISYKTEEKPI FSLDTVASAE SMSIYDDIDA DVLRNYQEYS LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAAL

UniProtKB: ATP synthase subunit gamma

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Macromolecule #5: ATP synthase F(1) complex subunit delta, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit delta, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.852506 KDa
SequenceString:
GQMSFTFASP TQVFFNGANV RQVDVPTQTG AFGILASHVP TLQVLRPGLV VVHAEDGTTS KYFVSSGSVT VNADSSVQLL AEEAVTLDM LDPGVAKANL EKAQSELLGA ADEASRAEIQ IRIEANEALV KAL

UniProtKB: ATP synthase F(1) complex subunit delta, mitochondrial

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Macromolecule #6: ATP synthase F1 subunit epsilon

MacromoleculeName: ATP synthase F1 subunit epsilon / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.242084 KDa
SequenceString:
VAYWRQAGLS YIRYSQICAK AVRDALKAEF KANAEKTSGS NVKIVKV

UniProtKB: ATP synthase F1 subunit epsilon

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Macromolecule #7: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.810329 KDa
SequenceString:
SSDTPEGVRS GAGAVRDAGG AFGKKEQADE ERYFRARARE QLAALKKHHE NEI

UniProtKB: ATPase inhibitor, mitochondrial

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Macromolecule #8: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 22.079689 KDa
SequenceString:
FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITAETFSA ISTIGVLVYI VKKYGASIGA FADKLNEQKI AQLEEVKQAS IKQIQDAID LEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYK EIKNRLDYHI SVQNMMRQKE QEHMIRWVEK H VVQSISAQ QEKETIAKCI ADLKLLAKKA QAQ

UniProtKB: ATP synthase subunit b

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Macromolecule #9: ATP synthase peripheral stalk subunit F6, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit F6, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 8.018009 KDa
SequenceString:
KLFVDKIREY RTKRQTSGGP VDAGPEYQQD LDRELFKLKQ MYGKADMNTF PNFTFEDPKF EAVEKPQS

UniProtKB: ATP synthase peripheral stalk subunit F6, mitochondrial

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Macromolecule #10: ATP synthase peripheral stalk subunit d, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit d, mitochondrial
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.904473 KDa
SequenceString:
RKLALKAIDW VAFGEIIPRN QKAIANSLKS WNETLSTRLA ALPEKPPAID WAYYKATVAK AGLVDDFEKK FNALKVPVPE DKYTALVDA EEQEDVKRCA EFLSLSKARI EAYEKELEKM KNIIPFDQMT IEDLNEVFPE TKLDKKKY

UniProtKB: ATP synthase peripheral stalk subunit d, mitochondrial

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Macromolecule #11: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 25.054143 KDa
SequenceString: MNENLFASFI APTMMGLPIV TLIIMFPSLL FPTPKRLINN RTISIQQWLI QLTSKQMMAI HNQKGQTWSL MLMSLIMFIG STNILGLLP HSFTPTTQLS MNLGMAIPLW SATVFTGFRY KTKTSLAHFL PQGTPALLIP MLVIIETISL FIQPVALAVR L TANITAGH ...String:
MNENLFASFI APTMMGLPIV TLIIMFPSLL FPTPKRLINN RTISIQQWLI QLTSKQMMAI HNQKGQTWSL MLMSLIMFIG STNILGLLP HSFTPTTQLS MNLGMAIPLW SATVFTGFRY KTKTSLAHFL PQGTPALLIP MLVIIETISL FIQPVALAVR L TANITAGH LLIHLIGGAT LALLNINTMT AFITFTILIL LTILEFAVAL IQAYVFTLLV SLYLHDNT

UniProtKB: ATP synthase F(0) complex subunit a

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Macromolecule #12: ATP synthase peripheral stalk subunit OSCP, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit OSCP, mitochondrial
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 20.561279 KDa
SequenceString:
FAKLVRPPVQ IYGIEGRYAT ALYSAASKQN KLEQVEKELL RVAQILKEPK VAASIMNPYV KRSVKVKSLS DMTAKEKFSP LTSNLINLL AENGRLSSTP GVISAFSTMM SVHRGEVPCS VTTASPLDEA TLTELKTVLK SFLSKGQILK LEVKVDPSIM G GMIVRIGE KYVDMSAKTK IQKLSRAMR

UniProtKB: ATP synthase peripheral stalk subunit OSCP, mitochondrial

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Macromolecule #13: ATP synthase F(0) complex subunit 8

MacromoleculeName: ATP synthase F(0) complex subunit 8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 2.639243 KDa
SequenceString:
FITITSMIMT LFILFQLKIS NY

UniProtKB: ATP synthase F(0) complex subunit 8

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Macromolecule #14: ATP synthase F(0) complex subunit f, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit f, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.940673 KDa
SequenceString:
VPLKDRRLLE VKLGELPSWI LMRDFTPSGI AGAFQRGYYR YYNKYVNVKK GSVAGLSMVL AAYVVFNYCR SYKELKHERL RKYH

UniProtKB: ATP synthase F(0) complex subunit f, mitochondrial

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

MacromoleculeName: ATP synthase F(0) complex subunit g, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 8.852386 KDa
SequenceString:
KPRLATFWHY AKVELVPPTP AEIPTAIQSL KKIVNSAQTG SFKQLTVKEA LLNGLVATEV LMWFYVGEII ARAQHGIPTI

UniProtKB: ATP synthase F(0) complex subunit g, mitochondrial

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Macromolecule #16: ATP synthase F(0) complex subunit e, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit e, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.361458 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGVAYGAKRY NYLKPRAEEE RRIAAEEKKK QDELK

UniProtKB: ATP synthase F(0) complex subunit e, mitochondrial

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Macromolecule #17: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 4 / 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 #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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

Concentration0.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105447
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model / Details: Genome annotation and AlphaFold
Output model

PDB-9pew:
Porcine ATP synthase with inhibitory protein IF1, DP-state

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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