[English] 日本語
Yorodumi
- PDB-8ap7: membrane region of the Trypanosoma brucei mitochondrial ATP synth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ap7
Titlemembrane region of the Trypanosoma brucei mitochondrial ATP synthase dimer
Components
  • ATP synthase subunit a
  • ATPEG3
  • ATPEG4
  • ATPTB1
  • ATPTB11
  • ATPTB12
  • ATPTB6
  • subunit-8
  • subunit-b
  • subunit-d
  • subunit-e
  • subunit-f
  • subunit-g
  • subunit-i/j
  • subunit-k
KeywordsMEMBRANE PROTEIN / ATP synthase / mitochondria
Function / homology
Function and homology information


kinetoplast / ATP biosynthetic process / ciliary plasm / nuclear lumen / proton-transporting ATP synthase complex / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / mitochondrion / membrane / cytoplasm
Similarity search - Function
CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / T. brucei spp.-specific protein / Uncharacterized protein / Transmembrane protein / ATP synthase subunit a / Uncharacterized protein / Letm1 RBD domain-containing protein ...CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-Q7G / T. brucei spp.-specific protein / Uncharacterized protein / Transmembrane protein / ATP synthase subunit a / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMuehleip, A. / Gahura, O. / Zikova, A. / Amunts, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2022
Title: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
Authors: Ondřej Gahura / Alexander Mühleip / Carolina Hierro-Yap / Brian Panicucci / Minal Jain / David Hollaus / Martina Slapničková / Alena Zíková / Alexey Amunts /
Abstract: Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM ...Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.
History
DepositionAug 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 26, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / em_software / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit a
C: subunit-8
D: subunit-d
E: ATPTB1
F: subunit-f
I: subunit-i/j
J: ATPTB6
K: subunit-k
L: subunit-e
M: subunit-g
N: ATPTB11
O: ATPTB12
P: subunit-b
Q: ATPEG3
R: ATPEG4
a: ATP synthase subunit a
c: subunit-8
d: subunit-d
e: ATPTB1
f: subunit-f
i: subunit-i/j
j: ATPTB6
k: subunit-k
l: subunit-e
m: subunit-g
n: ATPTB11
o: ATPTB12
p: subunit-b
q: ATPEG3
r: ATPEG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)622,78174
Polymers571,64330
Non-polymers51,13844
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area245750 Å2
ΔGint-1906 kcal/mol
Surface area164430 Å2

-
Components

-
Protein , 15 types, 30 molecules AaCcDdEeFfIiJjKkLlMmNnOoPpQqRr

#1: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 28708.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P24499
#2: Protein subunit-8


Mass: 13750.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585K5
#3: Protein subunit-d


Mass: 43379.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZW9
#4: Protein ATPTB1


Mass: 46883.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38CI8
#5: Protein subunit-f


Mass: 17182.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZE2
#6: Protein subunit-i/j


Mass: 12661.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57ZM4
#7: Protein ATPTB6


Mass: 20307.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A5R7
#8: Protein subunit-k


Mass: 14531.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57VT0
#9: Protein subunit-e


Mass: 10448.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q387J1
#10: Protein subunit-g


Mass: 16092.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZJA0
#11: Protein ATPTB11


Mass: 17929.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q582T1
#12: Protein ATPTB12


Mass: 11676.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57Z84
#13: Protein subunit-b


Mass: 12325.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZLR9
#14: Protein ATPEG3


Mass: 12293.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q583U4
#15: Protein ATPEG4


Mass: 7649.776 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister427

-
Sugars , 1 types, 4 molecules

#17: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 5 types, 64 molecules

#16: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#18: Chemical
ChemComp-Q7G / 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside


Mass: 1165.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H92O25
#19: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#20: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mitochondrial ATP synthase dimer from Trypanosoma brucei
Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister427 / Organelle: Mitochondrion
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingElectron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19rc4_4035: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100605 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00438912
ELECTRON MICROSCOPYf_angle_d0.45352063
ELECTRON MICROSCOPYf_dihedral_angle_d12.29715490
ELECTRON MICROSCOPYf_chiral_restr0.0355104
ELECTRON MICROSCOPYf_plane_restr0.0046210

+
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