[English] 日本語
Yorodumi
- EMDB-74155: Mitochondrial MDH and OSCP in the peripheral stalk of ATP synthas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74155
TitleMitochondrial MDH and OSCP in the peripheral stalk of ATP synthase in Acanthamoeba castellanii
Map data
Sample
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: mitochondrial ATP synthase subunit oscp
    • Protein or peptide: ACANB14707
Keywordscomplex V / OXPHOS / OXIDOREDUCTASE
Function / homology
Function and homology information


(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / malate metabolic process
Similarity search - Function
Malate dehydrogenase, type 2 / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(S)-malate dehydrogenase (NAD(+), oxaloacetate-forming)
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsFry MY / Luce BE / Stefely JA / Samuelson J / Mootha VK / Chao LH
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2026
Title: Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS.
Authors: Michelle Y Fry / Bridget E Luce / Jonathan A Stefely / Michael Z Chen / Felicia G Deng / Tiana M Issa / / Sarah E Calvo / John Samuelson / Vamsi K Mootha / Luke H Chao /
Abstract: Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have ...Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.
History
DepositionDec 2, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74155.png

Downloads & links

-
Map

FileDownload / File: emd_74155.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.27665183 - 0.4301827
Average (Standard dev.)0.0018842161 (±0.01656079)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 361.68002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_74155_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74155_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Acanthamoeba castellanii OXPHOS complex III intermediate assembly...

EntireName: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
Components
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: mitochondrial ATP synthase subunit oscp
    • Protein or peptide: ACANB14707

-
Supramolecule #1: Acanthamoeba castellanii OXPHOS complex III intermediate assembly...

SupramoleculeName: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 1.3 MDa

-
Macromolecule #1: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 1 / Details: ACANB11954 / Number of copies: 2 / Enantiomer: LEVO
EC number: (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 49.101977 KDa
SequenceString: MRRGLSTVSR SATVFGKQAC LASSTLRVDR RAYATSPEDA ALEAQIEKVL DLVKKQGNLG SEKLTVRKLT ELRQTVPEID RALSSVGDS AVKYMAELEK PGAGPLSAVP PVRVTVTGAA GAIGYAMLFR IASGEMLGKH QPVILQLLEL EPAMKALEGV I MELKDCAF ...String:
MRRGLSTVSR SATVFGKQAC LASSTLRVDR RAYATSPEDA ALEAQIEKVL DLVKKQGNLG SEKLTVRKLT ELRQTVPEID RALSSVGDS AVKYMAELEK PGAGPLSAVP PVRVTVTGAA GAIGYAMLFR IASGEMLGKH QPVILQLLEL EPAMKALEGV I MELKDCAF PLLHGVTASS DVNKAFEGAD FAMLVGAKPR TKGMERGDLL KENANIFSVQ GKALNKVANR DTLRVCVVGN PA NTNALIA SANAPNIHPR RFTAMTRLDH NRGIAQLADK LKCKVTDIER FAIWGNHSAT QYPDISHTQI NGKWAKDLVD EKW VKDTFI PDVQQRGAAI IAARGSSSAA SAANAAIEHM RDWVKGTNGQ WTSMGVWTGN GKVGDYGTSP DIYYSFPVVC ADGE YTIVQ NVPVDKFSAE RMQKTNDELV SEKNGVGELA KRTTDPAALL KEQYKGGKQ

UniProtKB: (S)-malate dehydrogenase (NAD(+), oxaloacetate-forming)

-
Macromolecule #2: mitochondrial ATP synthase subunit oscp

MacromoleculeName: mitochondrial ATP synthase subunit oscp / type: protein_or_peptide / ID: 2 / Details: ACANB01783 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 48.823629 KDa
SequenceString: MYASRSSGMA CRSRLASRVA PRMGNAARLV SARGFSQTLV TQQKKGEATT AAPVFKIDEE FDDYKDVTAS NEQVEKNYRE PPVQVTSGK HGEFASTLYA TASVLNAVED VERDLKWLVD ASQTIPMFQQ FLSSGLPDKK VMRKLLQGVL KGADFHRLTQ K FLVTELLE ...String:
MYASRSSGMA CRSRLASRVA PRMGNAARLV SARGFSQTLV TQQKKGEATT AAPVFKIDEE FDDYKDVTAS NEQVEKNYRE PPVQVTSGK HGEFASTLYA TASVLNAVED VERDLKWLVD ASQTIPMFQQ FLSSGLPDKK VMRKLLQGVL KGADFHRLTQ K FLVTELLE AGELKLVPDI AAVYAQIMKA HRKEVPVVFT FASLPDKDFL TRQIERVKKY RLEADATPMW EFKINPALIG GF TVEVGSN YKGNFALSSQ FDLMRQQLKQ AEDKWERVRP KELHINSFDT SSLFAPLSGV KITAADLDKT LADVLGSKKE AFQ AADLDR TLKQALEDAQ RDAGFSGDYE KNVLEQTRNL DFEKLKTVKQ LDLAQHEKHL MQKHNIADND AEGKRKVKAK IEEL KRFKE LDTSFIGEVL KKHQPETYKK YQSVFQ

-
Macromolecule #3: ACANB14707

MacromoleculeName: ACANB14707 / type: protein_or_peptide / ID: 3 / Details: ACANB14707 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 10.217619 KDa
SequenceString:
MSKRLITRAT LNGRLATAWA PSRSYAEAAV PKLGKDIQPK NYRRPDGTYE PCDEILFLSV IGYGEDLRAV TNAKEGITNT LVLSRYNKT ASQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.25 mg/mL
BufferpH: 7.9
Component:
ConcentrationName
50.0 mMHEPES
300.0 mMsodium chloride
4.0 mMmagnesium chloride
20.0 uMCalcium Chloride
1.0 mMDithiothreitol
0.5 % (w/v)DDM
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.14 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was not purified. Instead it was solved from imaging mitochondrial lysate.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 0.99 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v.4.7.0) / Software - details: Patch CTF estimation / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10863
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC / Software - details: ab initio reconstruction
Final angle assignmentType: PROJECTION MATCHING

+
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