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- EMDB-34580: Human ATP synthase state 1 (combined) -

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Basic information

Entry
Database: EMDB / ID: EMD-34580
TitleHuman ATP synthase state 1 (combined)
Map data
Sample
  • Complex: Human ATP synthase
    • Protein or peptide: x 17 types
  • Ligand: x 5 types
KeywordsATP synthase / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / : / negative regulation of mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / positive regulation of proteolysis involved in protein catabolic process / : / negative regulation of mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process / angiostatin binding / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of ATP-dependent activity / Mitochondrial protein import / ATPase inhibitor activity / mitochondrial depolarization / mitochondrial proton-transporting ATP synthase complex assembly / negative regulation of hydrolase activity / : / : / cellular response to interleukin-7 / oxidative phosphorylation / enzyme inhibitor activity / response to copper ion / response to muscle activity / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / negative regulation of endothelial cell proliferation / MHC class I protein binding / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / response to hyperoxia / H+-transporting two-sector ATPase / Mitochondrial protein degradation / proton-transporting ATPase activity, rotational mechanism / substantia nigra development / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / cellular response to dexamethasone stimulus / proton transmembrane transport / reactive oxygen species metabolic process / erythrocyte differentiation / generation of precursor metabolites and energy / regulation of intracellular pH / mitochondrial membrane / ADP binding / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / osteoblast differentiation / ATPase binding / protease binding / nuclear membrane / angiogenesis / response to ethanol / mitochondrial inner membrane / calmodulin binding / hydrolase activity / mitochondrial matrix / membrane raft / lipid binding / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / ATP synthase protein 8, metazoa / Mitochondrial ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted ...ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / Mitochondrial proteolipid / 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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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 d, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit delta, mitochondrial ...ATP synthase subunit d, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit e, mitochondrial / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLai Y / Zhang Y / Liu F / Gao Y / Gong H / Rao Z
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Mol Cell / Year: 2023
Title: Structure of the human ATP synthase.
Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
History
DepositionOct 25, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34580.png

Downloads & links

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Map

FileDownload / File: emd_34580.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-24.866976000000001 - 40.373722000000001
Average (Standard dev.)0.0032309238 (±1.0951303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human ATP synthase

EntireName: Human ATP synthase
Components
  • Complex: Human ATP synthase
    • 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 subunit d, mitochondrial
    • 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: ATPase inhibitor, mitochondrial
    • Protein or peptide: ATP synthase subunit O, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase subunit delta, mitochondrial
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit ATP5MJ, mitochondrial
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit g, mitochondrial
    • Protein or peptide: ATP synthase subunit e, mitochondrial
  • Ligand: CARDIOLIPIN
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Supramolecule #1: Human ATP synthase

SupramoleculeName: Human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.658586 KDa
SequenceString: PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK ...String:
PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK EQEHMINWVE KHVVQSISTQ QEKETIAKCI ADLKLLAKKA QAQPVM

UniProtKB: ATP synthase F(0) complex subunit B1, mitochondrial

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Macromolecule #2: ATP synthase-coupling factor 6, mitochondrial

MacromoleculeName: ATP synthase-coupling factor 6, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.606499 KDa
SequenceString:
MILQRLFRFS SVIRSAVSVH LRRNIGVTAV AFNKELDPIQ KLFVDKIREY KSKRQTSGGP VDASSEYQQE LERELFKLKQ MFGNADMNT FPTFKFEDPK FEVIEKPQA

UniProtKB: ATP synthase-coupling factor 6, mitochondrial

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Macromolecule #3: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.383982 KDa
SequenceString:
AGRKLALKTI DWVAFAEIIP QNQKAIASSL KSWNETLTSR LAALPENPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPV PEDKYTAQV DAEEKEDVKS CAEWVSLSKA RIVEYEKEME KMKNLIPFDQ MTIEDLNEAF PETKLDKKKY PYWPHQPIEN L

UniProtKB: ATP synthase subunit d, mitochondrial

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Macromolecule #4: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.27616 KDa
SequenceString: QKTGTAEMSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKTRRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII ...String:
QKTGTAEMSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKTRRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII GDRQTGKTSI AIDTIINQKR FNDGSDEKKK 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 NAFLSHVVSQ HQALL GTIR ADGKISEQSD AKLKEIVTNF LAGFEA

UniProtKB: ATP synthase subunit alpha, mitochondrial

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Macromolecule #5: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.821965 KDa
SequenceString: AQTSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPV GPETLGRIMN VIGEPIDERG PIKTKQFAPI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG G AGVGKTVL ...String:
AQTSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE GLVRGQKVLD SGAPIKIPV GPETLGRIMN VIGEPIDERG PIKTKQFAPI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AKGGKIGLFG G AGVGKTVL IMELINNVAK AHGGYSVFAG VGERTREGND LYHEMIESGV INLKDATSKV ALVYGQMNEP PGARARVALT GL TVAEYFR DQEGQDVLLF IDNIFRFTQA GSEVSALLGR IPSAVGYQPT LATDMGTMQE RITTTKKGSI TSVQAIYVPA DDL TDPAPA TTFAHLDATT VLSRAIAELG IYPAVDPLDS TSRIMDPNIV GSEHYDVARG VQKILQDYKS LQDIIAILGM DELS EEDKL TVSRARKIQR FLSQPFQVAE VFTGHMGKLV PLKETIKGFQ QILAGEYDHL PEQAFYMVGP IEEAVAKADK LAEEH SS

UniProtKB: ATP synthase subunit beta, mitochondrial

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Macromolecule #6: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.207752 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARIYGLGSLA LYEKADIKGP EDKKKHLLIG VSSDRGLCGA IHSSIAKQM KSEVATLTAA GKEVMLVGIG DKIRGILYRT HSDQFLVAFK EVGRKPPTFG DASVIALELL NSGYEFDEGS I IFNKFRSV ISYKTEEKPI FSLNTVASAD SMSIYDDIDA DVLQNYQEYN LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD

UniProtKB: ATP synthase subunit gamma, mitochondrial

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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: Homo sapiens (human)
Molecular weightTheoretical: 9.540627 KDa
SequenceString:
GSDQSENVDR GAGSIREAGG AFGKREQAEE ERYFRAQSRE QLAALKKHHE EEIVHHKKEI ERLQKEIERH KQKIKMLKHD D

UniProtKB: ATPase inhibitor, mitochondrial

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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: Homo sapiens (human)
Molecular weightTheoretical: 20.904488 KDa
SequenceString:
FAKLVRPPVQ VYGIEGRYAT ALYSAASKQN KLEQVEKELL RVAQILKEPK VAASVLNPYV KRSIKVKSLN DITAKERFSP LTTNLINLL AENGRLSNTQ GVVSAFSTMM SVHRGEVPCT VTSASPLEEA TLSELKTVLK SFLSQGQVLK LEAKTDPSIL G GMIVRIGE KYVDMSVKTK IQKLGRAMRE IV

UniProtKB: ATP synthase subunit O, mitochondrial

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Macromolecule #9: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.610954 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SLKQQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

UniProtKB: ATP synthase F(0) complex subunit C1, mitochondrial

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Macromolecule #10: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.029817 KDa
SequenceString:
AEAAAAPAAA SGPNQMSFTF ASPTQVFFNG ANVRQVDVPT LTGAFGILAA HVPTLQVLRP GLVVVHAEDG TTSKYFVSSG SIAVNADSS VQLLAEEAVT LDMLDLGAAK ANLEKAQAEL VGTADEATRA EIQIRIEANE ALVKALE

UniProtKB: ATP synthase subunit delta, mitochondrial

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Macromolecule #11: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.790779 KDa
SequenceString:
MVAYWRQAGL SYIRYSQICA KAVRDALKTE FKANAEKTSG SNVKIVKVKK E

UniProtKB: ATP synthase subunit epsilon, mitochondrial

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Macromolecule #12: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.833102 KDa
SequenceString: MNENLFASFI APTILGLPAA VLIILFPPLL IPTSKYLINN RLITTQQWLI KLTSKQMMTM HNTKGRTWSL MLVSLIIFIA TTNLLGLLP HSFTPTTQLS MNLAMAIPLW AGTVIMGFRS KIKNALAHFL PQGTPTPLIP MLVIIETISL LIQPMALAVR L TANITAGH ...String:
MNENLFASFI APTILGLPAA VLIILFPPLL IPTSKYLINN RLITTQQWLI KLTSKQMMTM HNTKGRTWSL MLVSLIIFIA TTNLLGLLP HSFTPTTQLS MNLAMAIPLW AGTVIMGFRS KIKNALAHFL PQGTPTPLIP MLVIIETISL LIQPMALAVR L TANITAGH LLMHLIGSAT LAMSTINLPS TLIIFTILIL LTILEIAVAL IQAYVFTLLV SLYLHDNT

UniProtKB: ATP synthase subunit a

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Macromolecule #13: ATP synthase subunit ATP5MJ, mitochondrial

MacromoleculeName: ATP synthase subunit ATP5MJ, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.673053 KDa
SequenceString:
MLQSIIKNIW IPMKPYYTKV YQEIWIGMGL MGFIVYKIRA ADKRSKALKA SAPAPGHH

UniProtKB: ATP synthase subunit ATP5MJ, mitochondrial

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Macromolecule #14: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.000634 KDa
SequenceString:
MPQLNTTVWP TMITPMLLTL FLITQLKMLN TNYHLPPSPK PMKMKNYNKP WEPKWTKICS LHSLPPQS

UniProtKB: ATP synthase protein 8

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Macromolecule #15: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.804686 KDa
SequenceString:
ASVGECPAPV PVKDKKLLEV KLGELPSWIL MRDFSPSGIF GAFQRGYYRY YNKYINVKKG SISGITMVLA CYVLFSYSFS YKHLKHERL RKYH

UniProtKB: ATP synthase subunit f, mitochondrial

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Macromolecule #16: ATP synthase subunit g, mitochondrial

MacromoleculeName: ATP synthase subunit g, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.309226 KDa
SequenceString:
AQFVRNLVEK TPALVNAAVT YSKPRLATFW YYAKVELVPP TPAEIPRAIQ SLKKIVNSAQ TGSFKQLTVK EAVLNGLVAT EVLMWFYVG EIIGKRGIIG YDV

UniProtKB: ATP synthase subunit g, mitochondrial

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Macromolecule #17: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.947215 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGVAYGATRY NYLKPRAEEE RRIAAEEKKK QDELKRIARE LAEDDSILK

UniProtKB: ATP synthase subunit e, mitochondrial

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Macromolecule #18: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 18 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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: 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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Macromolecule #22: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 22 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68388
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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