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- EMDB-7546: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7546
TitleMonomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
Map dataMonomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound
Sample
  • Complex: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
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) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSrivastava AP / Luo M / Symersky J / Liao MF / Mueller DM
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R01GM66223 United States
CitationJournal: Science / Year: 2018
Title: High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane.
Authors: Anurag P Srivastava / Min Luo / Wenchang Zhou / Jindrich Symersky / Dongyang Bai / Melissa G Chambers / José D Faraldo-Gómez / Maofu Liao / David M Mueller /
Abstract: Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo- ...Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F motor that rotates to drive ATP synthesis in the F subunit. We used single-particle cryo-electron microscopy (cryo-EM) to obtain structures of the full complex in a lipid bilayer in the absence or presence of the inhibitor oligomycin at 3.6- and 3.8-angstrom resolution, respectively. To limit conformational heterogeneity, we locked the rotor in a single conformation by fusing the F6 subunit of the stator with the δ subunit of the rotor. Assembly of the enzyme with the F6-δ fusion caused a twisting of the rotor and a 9° rotation of the F c-ring in the direction of ATP synthesis, relative to the structure of isolated F Our cryo-EM structures show how F and F are coupled, give insight into the proton translocation pathway, and show how oligomycin blocks ATP synthesis.
History
DepositionMar 13, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6cp3
  • Surface level: 0.03
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7546.png

Downloads & links

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Map

FileDownload / File: emd_7546.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy AUTHOR: 0.0324 / Movie #1: 0.03
Minimum - Maximum-0.08653326 - 0.15050863
Average (Standard dev.)-0.0000093551 (±0.005950946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0870.151-0.000

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Supplemental data

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Additional map: Additional map

Fileemd_7546_additional.map
AnnotationAdditional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with ...

EntireName: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
Components
  • Complex: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
    • Protein or peptide: ATP synthase subunit 9, 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 gamma, mitochondrial
    • Protein or peptide: ATP synthase subunit delta, mitochondrial
    • Protein or peptide: ATP synthase subunit epsilon, 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 protein 8
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit J, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with ...

SupramoleculeName: Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c

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Macromolecule #1: ATP synthase subunit 9, mitochondrial

MacromoleculeName: ATP synthase subunit 9, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.790385 KDa
SequenceString:
(FME)QLVLAAKYI GAGISTIGLL GAGIGIAIVF AALINGVSRN PSIKDTVFPM AILGFALSEA TGLFCLMVSF LLLFGV

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Macromolecule #2: ATP synthase subunit 5, mitochondrial

MacromoleculeName: ATP synthase subunit 5, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 20.901139 KDa
SequenceString: ASKAAAPPPV RLFGVEGTYA TALYQAAAKN SSIDAAFQSL QKVESTVKKN PKLGHLLLNP ALSLKDRNSV IDAIVETHKN LDGYVVNLL KVLSENNRLG CFEKIASDFG VLNDAHNGLL KGTVTSAEPL DPKSFKRIEK ALSASKLVGQ GKSLKLENVV K PEIKGGLI ...String:
ASKAAAPPPV RLFGVEGTYA TALYQAAAKN SSIDAAFQSL QKVESTVKKN PKLGHLLLNP ALSLKDRNSV IDAIVETHKN LDGYVVNLL KVLSENNRLG CFEKIASDFG VLNDAHNGLL KGTVTSAEPL DPKSFKRIEK ALSASKLVGQ GKSLKLENVV K PEIKGGLI VELGDKTVDL SISTKIQKLN KVLEDSI

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Macromolecule #3: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.007402 KDa
SequenceString: ASTKAQPTEV SSILEERIKG VSDEANLNET GRVLAVGDGI ARVFGLNNIQ AEELVEFSSG VKGMALNLEP GQVGIVLFGS DRLVKEGEL VKRTGNIVDV PVGPGLLGRV VDALGNPIDG KGPIDAAGRS RAQVKAPGIL PRRSVHEPVQ TGLKAVDALV P IGRGQREL ...String:
ASTKAQPTEV SSILEERIKG VSDEANLNET GRVLAVGDGI ARVFGLNNIQ AEELVEFSSG VKGMALNLEP GQVGIVLFGS DRLVKEGEL VKRTGNIVDV PVGPGLLGRV VDALGNPIDG KGPIDAAGRS RAQVKAPGIL PRRSVHEPVQ TGLKAVDALV P IGRGQREL IIGDRQTGKT AVALDTILNQ KRWNNGSDES KKLYCVYVAV GQKRSTVAQL VQTLEQHDAM KYSIIVAATA SE AAPLQYL APFTAASIGE WFRDNGKHAL IVYDDLSKQA VAYRQLSLLL RRPPGREAYP GDVFYLHSRL LERAAKLSEK EGS GSLTAL PVIETQGGDV SAYIPTNVIS ITDGQIFLEA ELFYKGIRPA INVGLSVSRV GSAAQVKALK QVAGSLKLFL AQYR EVAAF AQFGSDLDAS TKQTLVRGER LTQLLKQNQY SPLATEEQVP LIYAGVNGHL DGIELSRIGE FESSFLSYLK SNHNE LLTE IREKGELSKE LLASLKSATE SFVATF

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Macromolecule #4: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 51.181082 KDa
SequenceString: ASAAQSTPIT GKVTAVIGAI VDVHFEQSEL PAILNALEIK TPQGKLVLEV AQHLGENTVR TIAMDGTEGL VRGEKVLDTG GPISVPVGR ETLGRIINVI GEPIDERGPI KSKLRKPIHA DPPSFAEQST SAEILETGIK VVDLLAPYAR GGKIGLFGGA G VGKTVFIQ ...String:
ASAAQSTPIT GKVTAVIGAI VDVHFEQSEL PAILNALEIK TPQGKLVLEV AQHLGENTVR TIAMDGTEGL VRGEKVLDTG GPISVPVGR ETLGRIINVI GEPIDERGPI KSKLRKPIHA DPPSFAEQST SAEILETGIK VVDLLAPYAR GGKIGLFGGA G VGKTVFIQ ELINNIAKAH GGFSVFTGVG ERTREGNDLY REMKETGVIN LEGESKVALV FGQMNEPPGA RARVALTGLT IA EYFRDEE GQDVLLFIDN IFRFTQAGSE VSALLGRIPS AVGYQPTLAT DMGLLQERIT TTKKGSVTSV QAVYVPADDL TDP APATTF AHLDATTVLS RGISELGIYP AVDPLDSKSR LLDAAVVGQE HYDVASKVQE TLQTYKSLQD IIAILGMDEL SEQD KLTVE RARKIQRFLS QPFAVAEVFT GIPGKLVRLK DTVASFKAVL EGKYDNIPEH AFYMVGGIED VVAKAEKLAA EAN

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Macromolecule #5: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.65716 KDa
SequenceString: ATLKEVEMRL KSIKNIEKIT KTMKIVASTR LSKAEKAKIS AKKMDEAEQL FYKNAETKNL DVEATETGAP KELIVAITSD KGLCGSIHS QLAKAVRRHL NDQPNADIVT IGDKIKMQLL RTHPNNIKLS INGIGKDAPT FQESALIADK LLSVMKAGTY P KISIFYND ...String:
ATLKEVEMRL KSIKNIEKIT KTMKIVASTR LSKAEKAKIS AKKMDEAEQL FYKNAETKNL DVEATETGAP KELIVAITSD KGLCGSIHS QLAKAVRRHL NDQPNADIVT IGDKIKMQLL RTHPNNIKLS INGIGKDAPT FQESALIADK LLSVMKAGTY P KISIFYND PVSSLSFEPS EKPIFNAKTI EQSPSFGKFE IDTDANVPRD LFEYTLANQM LTAMAQGYAA EISARRNAMD NA SKNAGDM INRYSILYNR TRQAVITNEL VDIITGASSL G

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Macromolecule #6: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.565385 KDa
SequenceString:
AEAAAASSGL KLQFALPHET LYSGSEVTQV NLPAKSGRIG VLANHVPTVE QLLPGVVEVM EGSNSKKFFI SGGFATVQPD SQLCVTAIE AFPLESFSQE NIKNLLAEAK KNVSSSDARE AAEAAIQVEV LENLQSVLK

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Macromolecule #7: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.618359 KDa
SequenceString:
SAWRKAGISY AAYLNVAAQA IRSSLKTELQ TASVLNRSQT DAFYTQYKNG TAASEPTPIT K

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Macromolecule #8: ATP synthase subunit 4, mitochondrial

MacromoleculeName: ATP synthase subunit 4, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.194498 KDa
SequenceString: MSSTPEKQTD PKAKANSIIN AIPGNNILTK TGVLGTSAAA VIYAISNELY VINDESILLL TFLGFTGLVA KYLAPAYKDF ADARMKKVS DVLNASRNKH VEAVKDRIDS VSQLQNVAET TKVLFDVSKE TVELESEAFE LKQKVELAHE AKAVLDSWVR Y EASLRQLE ...String:
MSSTPEKQTD PKAKANSIIN AIPGNNILTK TGVLGTSAAA VIYAISNELY VINDESILLL TFLGFTGLVA KYLAPAYKDF ADARMKKVS DVLNASRNKH VEAVKDRIDS VSQLQNVAET TKVLFDVSKE TVELESEAFE LKQKVELAHE AKAVLDSWVR Y EASLRQLE QRQLAKSVIS RVQSELGNPK FQEKVLQQSI SEIEQLLSKL K

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Macromolecule #9: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.709424 KDa
SequenceString:
SLAKSAANKL DWAKVISSLR ITGSTATQLS SFKKRNDEAR RQLLELQSQP TEVDFSHYRS VLKNTSVIDK IESYVKQYKP VKIDASKQL QVIESFEKHA MTNAKETESL VSKELKDLQS TLDNIQSARP FDELTVDDLT KIKPEIDAKV EEMVKKGKWD V PGYKDRFG NLNVM

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Macromolecule #10: ATP synthase subunit H, mitochondrial

MacromoleculeName: ATP synthase subunit H, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.417298 KDa
SequenceString:
NVIQDLYLRE LKDTKLAPST LQDAEGNVKP WNPPQKPNLP ELELQGPEAL KAYTEQNVET AHVAKESEEG ESEPIEEDWL VLDDAEETK ESH

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Macromolecule #11: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.584166 KDa
SequenceString:
VSTLIPPKVV SSKNIGSAPN AKRIANVVHF YKSLPQGPAP AIKANTRLAR YKAKYFDGDN ASGKPLWHFA LGIIAFGYSM EYYFHLRHH KGAEEH

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Macromolecule #12: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.825215 KDa
SequenceString:
MPQLVPFYFM NQLTYGFLLM ITLLILFSQF FLPMILRLYV SRLFISKL

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Macromolecule #13: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.90043 KDa
SequenceString: SPLDQFEIRT LFGLQSSFID LSCLNLTTFS LYTIIVLLVI TSLYTLTNNN NKIIGSRWLI SQEAIYDTIM NMTKGQIGGK NWGLYFPMI FTLFMFIFIA NLISMIPYSF ALSAHLVFII SLSIVIWLGN TILGLYKHGW VFFSLFVPAG TPLPLVPLLV I IETLSYFA ...String:
SPLDQFEIRT LFGLQSSFID LSCLNLTTFS LYTIIVLLVI TSLYTLTNNN NKIIGSRWLI SQEAIYDTIM NMTKGQIGGK NWGLYFPMI FTLFMFIFIA NLISMIPYSF ALSAHLVFII SLSIVIWLGN TILGLYKHGW VFFSLFVPAG TPLPLVPLLV I IETLSYFA RAISLGLRLG SNILAGHLLM VILAGLTFNF MLINLFTLVF GFVPLAMILA IMMLEFAIGI IQGYVWAILT AS YLKDAVY LH

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Macromolecule #14: ATP synthase subunit J, mitochondrial

MacromoleculeName: ATP synthase subunit J, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.145884 KDa
SequenceString:
MLKRFPTPIL KVYWPFFVAG AAVYYGMSKA ADLSSNT

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Macromolecule #15: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1. mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 150 mM NaCl, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 91 %

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 105.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2896 / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 346399
CTF correctionSoftware - Name: RELION (ver. 1.4)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 104280
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6cp3:
Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • 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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