[English] 日本語
Yorodumi
- EMDB-28809: Yeast ATP synthase map in conformation-1 at pH 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28809
TitleYeast ATP synthase map in conformation-1 at pH 6
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: x 14 types
  • Ligand: x 3 types
KeywordsF-type ATP synthase / yeast / mitochondrial / MEMBRANE PROTEIN
Function / homology
Function and homology information


cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase ...cristae formation / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / 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, 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 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: 4.0 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 7, 2022-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28809.png

Downloads & links

-
Map

FileDownload / File: emd_28809.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.024215441 - 0.07478261
Average (Standard dev.)-0.000068763766 (±0.00397088)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_28809_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28809_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase
    • 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 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

+
Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#12, #1, #13-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: ATP synthase subunit 5, mitochondrial

MacromoleculeName: ATP synthase subunit 5, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.199393 KDa
SequenceString:
PPPVRLFGVE GTYATALYQA AAKNSSIDAA FQSLQKVEST VKKNPKLGHL LLNPALSLKD RNSVIDAIVE THKNLDGYVV NLLKVLSEN NRLGCFEKIA SDFGVLNDAH NGLLKGTVTS AEPLDPKSFK RIEKALSASK LVGQGKSLKL ENVVKPEIKG G LLVELGDK TVDLSISTKI QKLIKVLED

UniProtKB: ATP synthase subunit 5, mitochondrial

+
Macromolecule #2: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.984291 KDa
SequenceString: EVEMRLKSIN AIEKITKTMK IVASTRLSKA EKAKISAKKM DEAEQLFYKN AETKNLDKEL IVAITSDKGL CGSIHSQLAK AVRRHLNDQ PNADIVTIGD KIKMQLLRTH PNNIKLSING IGKDAPTFQE SALIADKLLS VMKAGTYPKI SIFYNDPVSS L SFEPSEKP ...String:
EVEMRLKSIN AIEKITKTMK 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

+
Macromolecule #3: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 3 / 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

+
Macromolecule #4: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 4 / 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

+
Macromolecule #5: ATP synthase subunit 4, mitochondrial

MacromoleculeName: ATP synthase subunit 4, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.561969 KDa
SequenceString:
NDESILLLTF LGFTGLVAKY LAPAYKDFAD ARMKKVSDVL NASRNKHVEA VKDRIDSVSQ LQNVAETTKV LFDVSKETVE LESEAFELK QKVELAHEAK AVLDSWVRYE ASLRQLEQRQ LAKSVVSRVQ SELGNPKFQE KVLQQSISEI EQLLSK

UniProtKB: ATP synthase subunit 4, mitochondrial

+
Macromolecule #6: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 6 / 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

+
Macromolecule #7: ATP synthase subunit H, mitochondrial

MacromoleculeName: ATP synthase subunit H, mitochondrial / type: protein_or_peptide / ID: 7 / 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

+
Macromolecule #8: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 8 / 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

+
Macromolecule #9: ATP synthase subunit 9, mitochondrial

MacromoleculeName: ATP synthase subunit 9, mitochondrial / type: protein_or_peptide / ID: 9 / 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

+
Macromolecule #10: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 10 / 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

+
Macromolecule #11: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: 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

+
Macromolecule #12: ATP synthase subunit J, mitochondrial

MacromoleculeName: ATP synthase subunit J, mitochondrial / type: protein_or_peptide / ID: 12 / 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

+
Macromolecule #13: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 13 / 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

+
Macromolecule #14: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 14 / 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

+
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

+
Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #17: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

7548

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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