[English] 日本語
Yorodumi
- PDB-7p3n: F1Fo-ATP synthase from Acinetobacter baumannii (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p3n
TitleF1Fo-ATP synthase from Acinetobacter baumannii (state 2)
Components(ATP synthase ...) x 8
KeywordsMEMBRANE PROTEIN / ATP synthase / ESKAPE / Rotary ATP synthase / F1Fo / peptidisc / bioenergetics / IMP / multi-drug resistance / pathogenic
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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. ...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, 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 / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit a / ATP synthase subunit c / ATP synthase subunit b / ATP synthase subunit delta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsDemmer, J.K. / Phillips, B.P. / Uhrig, O.L. / Filloux, A. / Allsopp, L.P. / Bublitz, M. / Meier, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT110068/Z/15/Z United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: Structure of ATP synthase from ESKAPE pathogen .
Authors: Julius K Demmer / Ben P Phillips / O Lisa Uhrig / Alain Filloux / Luke P Allsopp / Maike Bublitz / Thomas Meier /
Abstract: The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate ...The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate (ATP) synthase from in three distinct conformational states. The nucleotide-converting F subcomplex reveals a specific self-inhibition mechanism, which supports a unidirectional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded F complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next-generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen.
History
DepositionJul 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 16, 2022Group: Data collection / Category: em_imaging
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-13181
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13181
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit c
H: ATP synthase subunit c
J: ATP synthase subunit c
K: ATP synthase subunit c
L: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
R: ATP synthase subunit c
S: ATP synthase subunit c
a: ATP synthase subunit a
b: ATP synthase subunit b
d: ATP synthase subunit delta
e: ATP synthase epsilon chain
g: ATP synthase gamma chain
p: ATP synthase subunit b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,71430
Polymers533,66822
Non-polymers2,0468
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area86190 Å2
ΔGint-646 kcal/mol
Surface area198340 Å2

-
Components

-
ATP synthase ... , 8 types, 22 molecules ABCDEFGHJKLOPQRSabpdeg

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55452.906 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M142, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50327.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M144, H+-transporting two-sector ATPase
#3: Protein
ATP synthase subunit c / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 8363.021 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M139
#4: Protein ATP synthase subunit a / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 32467.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M137
#5: Protein ATP synthase subunit b / ATP synthase F(0) sector subunit b / ATPase subunit I / F-type ATPase subunit b / F-ATPase subunit b


Mass: 17009.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M140
#6: Protein ATP synthase subunit delta / ATP synthase F(1) sector subunit delta / F-type ATPase subunit delta / F-ATPase subunit delta


Mass: 19525.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M141
#7: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14551.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M145
#8: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 32135.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria)
References: UniProt: A3M143

-
Non-polymers , 3 types, 8 molecules

#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: F1Fo ATP synthase / Type: COMPLEX
Details: State 2 of F1Fo ATP synthase from ESKAPE pathogen Acinetobacter baumannii
Entity ID: #1-#8 / Source: NATURAL
Molecular weightValue: 0.528 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii ATCC 17978 (bacteria) / Cellular location: Cell membrane
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2150 mMPotassium ChlorideKCl1
32 mMMagnesium ChlorideMgCl2`1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was applied directly from gel filtration to ultra-thin carbon in peptidiscs.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: 4ul sample, blotted for 4s at a blotforce of -4.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Data collected at Diamond Light Source (Harwell, UK) using Titan Krios G3 and automated alignments using Sherpa. Detector used was Gatan K3 including energy filter.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 85000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11490
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategory
2EPU2.1image acquisition
4cryoSPARC2.15CTF correction
10cryoSPARC2.15initial Euler assignment
11cryoSPARC2.15final Euler assignment
12cryoSPARC2.15classification
13cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 349160
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26147 / Num. of class averages: 1 / Symmetry type: POINT

+
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