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- EMDB-28835: Yeast ATP synthase map in conformation-2, at pH 6 -

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Basic information

Entry
Database: EMDB / ID: EMD-28835
TitleYeast ATP synthase map in conformation-2, at pH 6
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
KeywordsF-type ATP synthase / yeast / mitochondrial / MEMBRANE PROTEIN
Function / homology
Function and homology information


cristae formation / mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis ...cristae formation / mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP synthase, F0 complex, subunit H / ATP synthase complex subunit h / ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain ...ATP synthase, F0 complex, subunit H / ATP synthase complex subunit h / ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / : / Fungal epsilon 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, 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 / 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 / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial ...ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit H, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSharma S / Patel H / Luo M / Mueller DM / Liao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F-F coupling.
Authors: Stuti Sharma / Min Luo / Hiral Patel / David M Mueller / Maofu Liao /
Abstract: Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at ...Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at neutral or basic pH have provided details of the reaction mechanism of ATP synthesis. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported. Here we use single-particle cryo-EM to analyze the conformational ensemble of the yeast (Saccharomyces cerevisiae) ATP synthase at pH 6. Of the four conformations resolved in this study, three are reaction intermediates. In addition to canonical catalytic dwell and binding dwell structures, we identify two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations. These structures provide new insights into the catalytic mechanism of the ATP synthase and highlight elastic coupling between the catalytic and proton translocating domains.
History
DepositionNov 9, 2022-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28835.png

Downloads & links

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Map

FileDownload / File: emd_28835.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.029357014 - 0.07799165
Average (Standard dev.)-0.00001476939 (±0.0040111607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28835_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit gamma, mitochondrial
    • Protein or peptide: ATP synthase subunit 4, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit H, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit 9, mitochondrial
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit J, mitochondrial
    • Protein or peptide: ATP synthase subunit 5, mitochondrial
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta, mitochondrial
    • Protein or peptide: ATP synthase subunit delta, mitochondrial
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.042393 KDa
SequenceString: EVEMRLKSIK NIEKITKTMK IVASTRLSKA EKAKISAKKM DEAEQLFYKN AETKNLDKEL IVAITSDKGL CGSIHSQLAK AVRRHLNDQ PNADIVTIGD KIKMQLLRTH PNNIKLSING IGKDAPTFQE SALIADKLLS VMKAGTYPKI SIFYNDPVSS L SFEPSEKP ...String:
EVEMRLKSIK NIEKITKTMK IVASTRLSKA EKAKISAKKM DEAEQLFYKN AETKNLDKEL IVAITSDKGL CGSIHSQLAK AVRRHLNDQ PNADIVTIGD KIKMQLLRTH PNNIKLSING IGKDAPTFQE SALIADKLLS VMKAGTYPKI SIFYNDPVSS L SFEPSEKP IFNAKTIEQS PSFGKFEIDT DANVPRDLFE YTLANQMLTA MAQGYAAEIS ARRNAMDNAS KNAGDMINRY SI LYNRTRQ AVITNELVDI ITGA

UniProtKB: ATP synthase subunit gamma, mitochondrial

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Macromolecule #2: ATP synthase subunit 4, mitochondrial

MacromoleculeName: ATP synthase subunit 4, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.575994 KDa
SequenceString:
NDESILLLTF LGFTGLVAKY LAPAYKDFAD ARMKKVSDVL NASRNKHVEA VKDRIDSVSQ LQNVAETTKV LFDVSKETVE LESEAFELK QKVELAHEAK AVLDSWVRYE ASLRQLEQRQ LAKSVISRVQ SELGNPKFQE KVLQQSISEI EQLLSK

UniProtKB: ATP synthase subunit 4, 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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.509188 KDa
SequenceString:
AKSAANKLDW AKVISSLRIT GSTATQLSSF KKRNDEARRQ LLELQSQPTE VDFSHYRSVL KNTSVIDKIE SYVKQYKPVK IDASKQLQV IESFEKHAMT NAKETESLVS KELKDLQSTL DNIQSARPFD ELTVDDLTKI KPEIDAKVEE MVKKGKWDVP G YKDRFGNL NVM

UniProtKB: ATP synthase subunit d, mitochondrial

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Macromolecule #4: ATP synthase subunit H, mitochondrial

MacromoleculeName: ATP synthase subunit H, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.090904 KDa
SequenceString:
QDLYLRELKD TKLAPSTLQD AEGNVKPWNP PQKPNLPELE LQGPEALKAY TEQNVETAHV AKESEEGESE PIEEDWLVLD DAEETKESH

UniProtKB: ATP synthase subunit H, mitochondrial

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Macromolecule #5: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.383837 KDa
SequenceString:
VSTLIPPKVV SSKNIGSAPN AKRIANVVHF YKSLPQGPAP AIKANTRLAR YKAKYFDGDN ASGKPLWHFA LGIIAFGYSM EYYFH

UniProtKB: ATP synthase subunit f, mitochondrial

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Macromolecule #6: ATP synthase subunit 9, mitochondrial

MacromoleculeName: ATP synthase subunit 9, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.663243 KDa
SequenceString:
MQLVLAAKYI GAGISTIGLL GAGIGIAIVF AALINGVSRN PSIKDTVFPM AILGFALSEA TGLFCLMVSF LLLFG

UniProtKB: ATP synthase subunit 9, mitochondrial

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Macromolecule #7: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.046215 KDa
SequenceString:
FYFMNQLTYG FLLMITLLIL FSQFFLPMIL RLYVSRLFIS K

UniProtKB: ATP synthase protein 8

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Macromolecule #8: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.07323 KDa
SequenceString: LTTFSLYTII VLLVITSLYT LTNNNNKIIG SRWLISQEAI YDTIMNMTKG QIGGKNWGLY FPMIFTLFMF IFIANLISMI PYSFALSAH LVFIISLSIV IWLGNTILGL YKHGWVFFSL FVPAGTPLPL VPLLVIIETL SYFARAISLG LRLGSNILAG H LLMVILAG ...String:
LTTFSLYTII VLLVITSLYT LTNNNNKIIG SRWLISQEAI YDTIMNMTKG QIGGKNWGLY FPMIFTLFMF IFIANLISMI PYSFALSAH LVFIISLSIV IWLGNTILGL YKHGWVFFSL FVPAGTPLPL VPLLVIIETL SYFARAISLG LRLGSNILAG H LLMVILAG LTFNFMLINL FTLVFGFVPL AMILAIMMLE FAIGIIQGYV WAILTASYLK DAVYLH

UniProtKB: ATP synthase subunit a

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Macromolecule #9: ATP synthase subunit J, mitochondrial

MacromoleculeName: ATP synthase subunit J, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 4.145884 KDa
SequenceString:
MLKRFPTPIL KVYWPFFVAG AAVYYGMSKA ADLSSNT

UniProtKB: ATP synthase subunit J, mitochondrial

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Macromolecule #10: ATP synthase subunit 5, mitochondrial

MacromoleculeName: ATP synthase subunit 5, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.826584 KDa
SequenceString:
PPPVRLFGVE GTYATALYQA AAKNSSIDAA FQSLQKVEST VKKNPKLGHL LLNPALSLKD RNSVIDAIVE THKNLDGYVV NLLKVLSEN NRLGCFEKIA SDFGVLNDAH NGLLKGTVTS AEPLDPKSFK RIEKALSASK LVGQGKSLKL ENVVKPEIKG G LIVELG

UniProtKB: ATP synthase subunit 5, mitochondrial

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Macromolecule #11: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.748148 KDa
SequenceString: KAQPTEVSSI LEERIKGVSD EANLNETGRV LAVGDGIARV FGLNNIQAEE LVEFSSGVKG MALNLEPGQV GIVLFGSDRL VKEGELVKR TGNIVDVPVG PGLLGRVVDA LGNPIDGKGP IDAAGRSRAQ VKAPGILPRR SVHEPVQTGL KAVDALVPIG R GQRELIIG ...String:
KAQPTEVSSI LEERIKGVSD EANLNETGRV LAVGDGIARV FGLNNIQAEE LVEFSSGVKG MALNLEPGQV GIVLFGSDRL VKEGELVKR TGNIVDVPVG PGLLGRVVDA LGNPIDGKGP IDAAGRSRAQ VKAPGILPRR SVHEPVQTGL KAVDALVPIG R GQRELIIG DRQTGKTAVA LDTILNQKRW NNGSDESKKL YCVYVAVGQK RSTVAQLVQT LEQHDAMKYS IIVAATASEA AP LQYLAPF TAASIGEWFR DNGKHALIVY DDLSKQAVAY RQLSLLLRRP PGREAYPGDV FYLHSRLLER AAKLSEKEGS GSL TALPVI ETQGGDVSAY IPTNVISITD GQIFLEAELF YKGIRPAINV GLSVSRVGSA AQVKALKQVA GSLKLFLAQY REVA AFAQF GSDLDASTKQ TLVRGERLTQ LLKQNQYSPL ATEEQVPLIY AGVNGHLDGI ELSRIGEFES SFLSYLKSNH NELLT EIRE KGELSKELLA SLKSATESFV ATF

UniProtKB: ATP synthase subunit alpha, mitochondrial

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Macromolecule #12: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.752641 KDa
SequenceString: STPITGKVTA VIGAIVDVHF EQSELPAILN ALEIKTPQGK LVLEVAQHLG ENTVRTIAMD GTEGLVRGEK VLDTGGPISV PVGRETLGR IINVIGEPID ERGPIKSKLR KPIHADPPSF AEQSTSAEIL ETGIKVVDLL APYARGGKIG LFGGAGVGKT V FIQELINN ...String:
STPITGKVTA VIGAIVDVHF EQSELPAILN ALEIKTPQGK LVLEVAQHLG ENTVRTIAMD GTEGLVRGEK VLDTGGPISV PVGRETLGR IINVIGEPID ERGPIKSKLR KPIHADPPSF AEQSTSAEIL ETGIKVVDLL APYARGGKIG LFGGAGVGKT V FIQELINN IAKAHGGFSV FTGVGERTRE GNDLYREMKE TGVINLEGES KVALVFGQMN EPPGARARVA LTGLTIAEYF RD EEGQDVL LFIDNIFRFT QAGSEVSALL GRIPSAVGYQ PTLATDMGLL QERITTTKKG SVTSVQAVYV PADDLTDPAP ATT FAHLDA TTVLSRGISE LGIYPAVDPL DSKSRLLDAA VVGQEHYDVA SKVQETLQTY KSLQDIIAIL GMDELSEQDK LTVE RARKI QRFLSQPFAV AEVFTGIPGK LVRLKDTVAS FKAVLEGKYD NIPEHAFYMV GGIEDVVAKA EKLAAEAN

UniProtKB: ATP synthase subunit beta, mitochondrial

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Macromolecule #13: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.080876 KDa
SequenceString:
SSGLKLQFAL PHETLYSGSE VTQVNLPAKS GRIGVLANHV PTVEQLLPGV VEVMEGSNSK KFFISGGFAT VQPDSQLCVT AIEAFPLES FSQENIKNLL AEAKKNVSSS DAREAAEAAI QVEVLENLQS VLK

UniProtKB: ATP synthase subunit delta, mitochondrial

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Macromolecule #14: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.388076 KDa
SequenceString:
SAWRKAGISY AAYLNVAAQA IRSSLKTELQ TASVLNRSQT DAFYTQYKNG TAASEPTPI

UniProtKB: ATP synthase subunit epsilon, mitochondrial

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Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7548

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99780

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