[English] 日本語
Yorodumi
- EMDB-25947: Yeast ATP synthase State 1catalytic(b) without exogenous ATP back... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25947
TitleYeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model
Map dataUnsharpened map.
Sample
  • Complex: Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model
    • Protein or peptide: x 14 types
KeywordsF1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex
Function / homology
Function and homology information


: / : / cristae formation / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton-transporting ATP synthase complex / proton transmembrane transporter activity / mitochondrial nucleoid / proton motive force-driven ATP synthesis ...: / : / cristae formation / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton-transporting ATP synthase complex / proton transmembrane transporter activity / mitochondrial nucleoid / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / ATP 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit 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 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 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: 4.4 Å
AuthorsGuo H / Rubinstein JL
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canada Research ChairsElectron Cryomicroscopy Canada
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canada Foundation for Innovation Canada
Citation
Journal: Nat Commun / Year: 2022
Title: Structure of ATP synthase under strain during catalysis.
Authors: Hui Guo / John L Rubinstein /
Abstract: ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor ...ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F or proton translocation through F, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F, leading to catalysis.
#1: Journal: Biorxiv / Year: 2022
Title: Structure of ATP synthase under strain during catalysis
Authors: Guo H / Rubinstein JL
History
DepositionJan 17, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25947.png

Downloads & links

-
Map

FileDownload / File: emd_25947.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 256 pix.
= 344.96 Å		1.35 Å/pix.
x 256 pix.
= 344.96 Å		1.35 Å/pix.
x 256 pix.
= 344.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3475 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-0.53835803 - 1.7915299
Average (Standard dev.)0.003443865 (±0.10449573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 344.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_25947_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_25947_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_25947_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Yeast ATP synthase State 1catalytic(b) without exogenous ATP back...

EntireName: Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model
Components
  • Complex: Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model
    • Protein or peptide: ATP synthase subunit 9
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: ATP synthase subunit 5
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit 4
    • Protein or peptide: ATP synthase subunit d
    • Protein or peptide: ATP synthase subunit f
    • Protein or peptide: ATP synthase subunit H
    • Protein or peptide: ATP synthase subunit J
    • Protein or peptide: ATP synthase protein 8

+
Supramolecule #1: Yeast ATP synthase State 1catalytic(b) without exogenous ATP back...

SupramoleculeName: Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 610 KDa

+
Macromolecule #1: ATP synthase subunit 9

MacromoleculeName: ATP synthase subunit 9 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 7.762375 KDa
SequenceString:
MQLVLAAKYI GAGISTIGLL GAGIGIAIVF AALINGVSRN PSIKDTVFPM AILGFALSEA TGLFCLMVSF LLLFGV

UniProtKB: ATP synthase subunit 9, mitochondrial

+
Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit alpha, mitochondrial

+
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: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit beta, mitochondrial

+
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: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit gamma, mitochondrial

+
Macromolecule #5: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 14.565385 KDa
SequenceString:
AEAAAASSGL KLQFALPHET LYSGSEVTQV NLPAKSGRIG VLANHVPTVE QLLPGVVEVM EGSNSKKFFI SGGFATVQPD SQLCVTAIE AFPLESFSQE NIKNLLAEAK KNVSSSDARE AAEAAIQVEV LENLQSVLK

UniProtKB: ATP synthase subunit delta, mitochondrial

+
Macromolecule #6: ATP synthase subunit epsilon

MacromoleculeName: ATP synthase subunit epsilon / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 6.618359 KDa
SequenceString:
SAWRKAGISY AAYLNVAAQA IRSSLKTELQ TASVLNRSQT DAFYTQYKNG TAASEPTPIT K

UniProtKB: ATP synthase subunit epsilon, mitochondrial

+
Macromolecule #7: ATP synthase subunit 5

MacromoleculeName: ATP synthase subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit 5, mitochondrial

+
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) / Strain: USY006
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

UniProtKB: ATP synthase subunit a

+
Macromolecule #9: ATP synthase subunit 4

MacromoleculeName: ATP synthase subunit 4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit 4, mitochondrial

+
Macromolecule #10: ATP synthase subunit d

MacromoleculeName: ATP synthase subunit d / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
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

UniProtKB: ATP synthase subunit d, mitochondrial

+
Macromolecule #11: ATP synthase subunit f

MacromoleculeName: ATP synthase subunit f / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 10.584166 KDa
SequenceString:
VSTLIPPKVV SSKNIGSAPN AKRIANVVHF YKSLPQGPAP AIKANTRLAR YKAKYFDGDN ASGKPLWHFA LGIIAFGYSM EYYFHLRHH KGAEEH

UniProtKB: ATP synthase subunit f, mitochondrial

+
Macromolecule #12: ATP synthase subunit H

MacromoleculeName: ATP synthase subunit H / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 10.417298 KDa
SequenceString:
NVIQDLYLRE LKDTKLAPST LQDAEGNVKP WNPPQKPNLP ELELQGPEAL KAYTEQNVET AHVAKESEEG ESEPIEEDWL VLDDAEETK ESH

UniProtKB: ATP synthase subunit H, mitochondrial

+
Macromolecule #13: ATP synthase subunit J

MacromoleculeName: ATP synthase subunit J / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 6.696771 KDa
SequenceString:
MLKRFPTPIL KVYWPFFVAG AAVYYGMSKA ADLSSNTKEF INDPRNPRFA KGGKFVEVD

UniProtKB: ATP synthase subunit J, mitochondrial

+
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: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 5.825215 KDa
SequenceString:
MPQLVPFYFM NQLTYGFLLM ITLLILFSQF FLPMILRLYV SRLFISKL

UniProtKB: ATP synthase protein 8

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8817 / Average exposure time: 10.1 sec. / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 133843 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 442025
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 8810
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.1.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.1.0)
Final 3D classificationNumber classes: 9 / Avg.num./class: 42000 / Software - Name: cryoSPARC (ver. 3.1.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2hld


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-7tjz:
Yeast ATP synthase State 1catalytic(b) without exogenous ATP backbone model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more