[English] 日本語
Yorodumi
- EMDB-8359: Autoinhibited E. coli ATP synthase state 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8359
TitleAutoinhibited E. coli ATP synthase state 3
Map dataAutoinhibited E. coli ATP synthase state 3
Sample
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit c
    • Ligand: ADENOSINE-5'-TRIPHOSPHATE
    • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP synthase / ATPase / rotary motor / membrane protein / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity ...proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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 a / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit c / ATP synthase epsilon chain / ATP synthase subunit a / ATP synthase subunit b ...ATP synthase subunit a / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit c / ATP synthase epsilon chain / ATP synthase subunit a / ATP synthase subunit b / ATP synthase subunit b / ATP synthase subunit delta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit beta / ATP synthase subunit c
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.53 Å
AuthorsSobti M / Smits C / Wong AS / Ishmukhametov R / Stock D / Sandin S / Stewart AG
CitationJournal: Elife / Year: 2016
Title: Cryo-EM structures of the autoinhibitedE. coliATP synthase in three rotational states.
Authors: Sobti M / Smits C / Wong AS / Ishmukhametov R / Stock D / Sandin S / Stewart AG
History
DepositionAug 29, 2016-
Header (metadata) releaseJan 4, 2017-
Map releaseJan 4, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5t4q
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

-
Map

FileDownload / File: emd_8359.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAutoinhibited E. coli ATP synthase state 3
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.045
Minimum - Maximum-0.02577311 - 0.1047882
Average (Standard dev.)-0.00014185307 (±0.009308554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 350.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z350.000350.000350.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0260.105-0.000

-
Supplemental data

-
Sample components

+
Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit c
    • Ligand: ADENOSINE-5'-TRIPHOSPHATE
    • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 558 KDa

+
Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 55.138531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLNSTEISE LIKQRIAQFN VVSEAHNEGT IVSVSDGVIR IHGLADAMQG EMISLPGNRY AIALNLERDS VGAVVMGPYA DLAEGMKVK ATGRILEVPV GRGLLGRVVN TLGAPIDGKG PLDHDGFSAV EAIAPGVIER QSVDQPVQTG YKAVDSMIPI G RGQRELII ...String:
MQLNSTEISE LIKQRIAQFN VVSEAHNEGT IVSVSDGVIR IHGLADAMQG EMISLPGNRY AIALNLERDS VGAVVMGPYA DLAEGMKVK ATGRILEVPV GRGLLGRVVN TLGAPIDGKG PLDHDGFSAV EAIAPGVIER QSVDQPVQTG YKAVDSMIPI G RGQRELII GDRQTGKTAL AIDAIINQRD SGIKAIYVAI GQKASTISNV VRKLEEHGAL ANTIVVVATA SESAALQYLA PY AGAAMGE YFRDRGEDAL IIYDDLSKQA VAYRQISLLL RRPPGREAFP GDVFYLHSRL LERAARVNAE YVEAFTKGEV KGK TGSLTA LPIIETQAGD VSAFVPTNVI SITDGQIFLE TNLFNAGIRP AVNPGISVSR VGGAAQTKIM KKLSGGIRTA LAQY RELAA FSQFASDLDD ATRNQLDHGQ KVTELLKQKQ YAPMSVAQQS LVLFAAERGY LADVELSKIG SFEAALLAYV DRDHA PLMQ EINQTGGYND EIEGKLKGIL DSFKATQSW

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 51.664574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GMATGKIVQV IGAVVDVEFP QDAVPRVYDA LEVQNGNERL VLEVQQQLGG GIVRTIAMGS SDGLRRGLDV KDLEHPIEV PVGKATLGRI MNVLGEPVDM KGEIGEEERW AIHRAAPSYE ELSNSQELLE TGIKVIDLMA PFAKGGKVGL F GGAGVGKT ...String:
MRGSHHHHHH GMATGKIVQV IGAVVDVEFP QDAVPRVYDA LEVQNGNERL VLEVQQQLGG GIVRTIAMGS SDGLRRGLDV KDLEHPIEV PVGKATLGRI MNVLGEPVDM KGEIGEEERW AIHRAAPSYE ELSNSQELLE TGIKVIDLMA PFAKGGKVGL F GGAGVGKT VNMMELIRNI AIEHSGYSVF AGVGERTREG NDFYHEMTDS NVIDKVSLVY GQMNEPPGNR LRVALTGLTM AE KFRDEGR DVLLFVDNIY RYTLAGTEVS ALLGRMPSAV GYQPTLAEEM GVLQERITST KTGSITSVQA VYVPADDLTD PSP ATTFAH LDATVVLSRQ IASLGIYPAV DPLDSTSRQL DPLVVGQEHY DTARGVQSIL QRYQELKDII AILGMDELSE EDKL VVARA RKIQRFLSQP FFVAEVFTGS PGKYVSLKDT IRGFKGIMEG EYDHLPEQAF YMVGSIEEAV EKAKKL

UniProtKB: ATP synthase subunit beta

+
Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.539285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGAKDIRSK IASVQNTQKI TKAMEMVAAS KMRKSQDRMA ASRPYAETMR KVIGHLAHGN LEYKHPYLED RDVKRVGYLV VSTDRGLAG GLNINLFKKL LAEMKTWTDK GVQADLAMIG SKGVSFFNSV GGNVVAQVTG MGDNPSLSEL IGPVKVMLQA Y DEGRLDKL ...String:
MAGAKDIRSK IASVQNTQKI TKAMEMVAAS KMRKSQDRMA ASRPYAETMR KVIGHLAHGN LEYKHPYLED RDVKRVGYLV VSTDRGLAG GLNINLFKKL LAEMKTWTDK GVQADLAMIG SKGVSFFNSV GGNVVAQVTG MGDNPSLSEL IGPVKVMLQA Y DEGRLDKL YIVSNKFINT MSQVPTISQL LPLPASDDDD LKHKSWDYLY EPDPKALLDT LLRRYVESQV YQGVVENLAS EQ AARMVAM KAATDNGGSL IKELQLVYNK ARQASITQEL TEIVSGAAAV

UniProtKB: ATP synthase gamma chain

+
Macromolecule #4: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.087244 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAMTYHLDVV SAEQQMFSGL VEKIQVTGSE GELGIYPGHA PLLTAIKPGM IRIVKQHGHE EFIYLSGGIL EVQPGNVTVL ADTAIRGQD LDEARAMEAK RKAEEHISSS HGDVDYAQAS AELAKAIAQL RVIELTKKAM

UniProtKB: ATP synthase epsilon chain

+
Macromolecule #5: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.126691 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NLNATILGQA IAFVLFVLFA MKYVWPPLMA AIEKRQKEIA DGLASAERAH KDLDLAKASA TDQLKKAKAE AQVIIEQANK RRSQILDEA KAEAEQERTK IVAQAQAEIE AERKRAREEL RKQVAILAVA GAEKIIERSV DEAANSDIVD KLVAEL

UniProtKB: ATP synthase subunit b

+
Macromolecule #6: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.324096 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASENMTPQD YIGHHLNNLQ LDLRTFSLVD PQNPPATFWT INIDSMFFSV VLGLLFLVLF RSVAKKATSG VPGKFQTAIE LVIGFVNGS VKDMYHGKSK LIAPLALTIF VWVFLMNLMD LLPIDLLPYI AEHVLGLPAL RVVPSADVNV TLSMALGVFI L ILFYSIKM ...String:
MASENMTPQD YIGHHLNNLQ LDLRTFSLVD PQNPPATFWT INIDSMFFSV VLGLLFLVLF RSVAKKATSG VPGKFQTAIE LVIGFVNGS VKDMYHGKSK LIAPLALTIF VWVFLMNLMD LLPIDLLPYI AEHVLGLPAL RVVPSADVNV TLSMALGVFI L ILFYSIKM KGIGGFTKEL TLQPFNHWAF IPVNLILEGV SLLSKPVSLG LRLFGNMYAG ELIFILIAGL LPWWSQWILN VP WAIFHIL IITLQAFIFM VLTIVYLSMA SEEH

UniProtKB: ATP synthase subunit a

+
Macromolecule #7: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 19.289061 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSEFITVARP YAKAAFDFAV EHQSVERWQD MLAFAAEVTK NEQMAELLSG ALAPETLAES FIAVAGEQLD ENGQNLIRVM AENGRLNAL PDVLEQFIHL RAVSEATAEV DVISAAALSE QQLAKISAAM EKRLSRKVKL NAKIDKSVMA GVIIRAGDMV I DGSVRGRL ERLADVLQS

UniProtKB: ATP synthase subunit delta

+
Macromolecule #8: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 8 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.259064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MENLNMDLLY MAAAVMMGLA AIGAAIGIGI LGGKFLEGAA RQPDLIPLLR TQFFIVMGLV DAIPMIAVGL GLYVMFAVA

UniProtKB: ATP synthase subunit c

+
Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 29.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: Model from previous dataset
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95345
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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