[English] 日本語
Yorodumi
- EMDB-73974: Cryo-EM structure of Leishmania tarentolae respiratory complex V ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73974
TitleCryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) membrane region
Map data
Sample
  • Complex: membrane region of Leishmania tarentolae ATP synthase
    • Protein or peptide: x 15 types
KeywordsElectron transport chain / respiratory complex / ATP synthase / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / ATPase 6
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsLiao YT / Chao L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2026
Title: Conserved and divergent mitochondrial assemblies in kinetoplastid parasites
Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M ...Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M / Lian CG / Luce BE / Mian SY / Nguyen K / Paul AS / Samuelson J / Stefely JA / Udeshi ND / Mootha VK / Aphasizheva I / Chao LH / Aphasizhev R
History
DepositionNov 20, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73974.png

Downloads & links

-
Map

FileDownload / File: emd_73974.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 768 pix.
= 565.248 Å		0.74 Å/pix.
x 768 pix.
= 565.248 Å		0.74 Å/pix.
x 768 pix.
= 565.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.10791455 - 0.21157
Average (Standard dev.)0.00057044293 (±0.008889791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 565.248 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_73974_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_73974_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73974_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_73974_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : membrane region of Leishmania tarentolae ATP synthase

EntireName: membrane region of Leishmania tarentolae ATP synthase
Components
  • Complex: membrane region of Leishmania tarentolae ATP synthase
    • Protein or peptide: LtaP27_632926_633111, LtATPEG4
    • Protein or peptide: Mitochondrial ATP synthase subunit c-1
    • Protein or peptide: ATPase 6
    • Protein or peptide: Mitochondrial ATP synthase subunit i/j
    • Protein or peptide: Mitochondrial ATP synthase subunit ATPTB1
    • Protein or peptide: Mitochondrial ATP synthase subunit ATPTB6
    • Protein or peptide: Mitochondrial ATP synthase subunit g
    • Protein or peptide: Mitochondrial ATP synthase subunit f
    • Protein or peptide: Mitochondrial ATP synthase subunit 8
    • Protein or peptide: Mitochondrial ATP synthase subunit b
    • Protein or peptide: Mitochondrial ATP synthase subunit e
    • Protein or peptide: Mitochondrial ATP synthase subunit k
    • Protein or peptide: Mitochondrial ATP synthase subunit ATPTB12
    • Protein or peptide: Mitochondrial ATP synthase subunit ATPTB11
    • Protein or peptide: Mitochondrial ATP synthase subunit ATPEG3

+
Supramolecule #1: membrane region of Leishmania tarentolae ATP synthase

SupramoleculeName: membrane region of Leishmania tarentolae ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, ...Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, followed by centrifuging at 14,000 x g for 10 min. The supernatant was filtered prior to grid preparation.
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)

+
Macromolecule #1: LtaP27_632926_633111, LtATPEG4

MacromoleculeName: LtaP27_632926_633111, LtATPEG4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 6.756731 KDa
SequenceString:
GFVPRRFAQF NRDPWWMFFI FSIGAWVGEY PAMQIKYNAR DLVLDPHRYV WSHLD

+
Macromolecule #2: Mitochondrial ATP synthase subunit c-1

MacromoleculeName: Mitochondrial ATP synthase subunit c-1 / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 7.854518 KDa
SequenceString:
VAISIQGLHY VGTGLGAIAL GGVGMGIGTI FGCLLIACAR QPNLTKMLFN YAILGFALTE AIGLFALMLA FLMLFS

+
Macromolecule #3: ATPase 6

MacromoleculeName: ATPase 6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 28.261975 KDa
SequenceString: MFVFFVCDLV IMRILLCFCY SVWSRIIFVL FYNVFYICTE LMFCIFDVYL FVGLCMFICL WFVLFNFYGL IVYYCITYLN VYILFCIVF MYYMAFLFCF CFLLDFILFG SLLVGDAFMD VFFLRYLLCV LECFSLLCRC ISTFLRMFCN LLSSHFLMLM F CDFVYFFI ...String:
MFVFFVCDLV IMRILLCFCY SVWSRIIFVL FYNVFYICTE LMFCIFDVYL FVGLCMFICL WFVLFNFYGL IVYYCITYLN VYILFCIVF MYYMAFLFCF CFLLDFILFG SLLVGDAFMD VFFLRYLLCV LECFSLLCRC ISTFLRMFCN LLSSHFLMLM F CDFVYFFI IFFLFFIMCD FIYFIIFTFA MLFCIIFYLF LYALDMFCAL LQIFIFCNMI MQLIMDFLLL LSF

UniProtKB: ATPase 6

+
Macromolecule #4: Mitochondrial ATP synthase subunit i/j

MacromoleculeName: Mitochondrial ATP synthase subunit i/j / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 12.293158 KDa
SequenceString:
VYTRWKCDRI PVLQLKLFTQ EYNIMALVGL LSMVFLFKHA SYCSEETERK NGWWAGYPYW RDPIARRNEI RYKQLINSND VDITDPKWT GCSKEQLERL RAI

UniProtKB: Uncharacterized protein

+
Macromolecule #5: Mitochondrial ATP synthase subunit ATPTB1

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 45.347246 KDa
SequenceString: MQGTWSVLKK NCLNFVPGLA LFASQSRDAF ATWMKIYNRG YKYGPQEFSD QAEAYTPDYW KRGHSQEKNM WVDMKLSEEV SQKELAQLM HYKQDLWRMG HGLGLSLFLG GYALIPAFFC LSSDTFAPSC FCKTEEEKKA WREAQDMYRY RSAPSYIMDT K WHFDFHAY ...String:
MQGTWSVLKK NCLNFVPGLA LFASQSRDAF ATWMKIYNRG YKYGPQEFSD QAEAYTPDYW KRGHSQEKNM WVDMKLSEEV SQKELAQLM HYKQDLWRMG HGLGLSLFLG GYALIPAFFC LSSDTFAPSC FCKTEEEKKA WREAQDMYRY RSAPSYIMDT K WHFDFHAY PWNATQERAW DDLFEKNNVR RDPKVLRPAA EMYDGFLKFY QIRRKSLRHL ARSMNLPTFP LLSRTCASTR VK DYWNLAW NEDYMVITQK LHHQMSDEDL HDYAWRRFLA PYDKNLSRDE IMTRVNDYHE FLGPKFVEEG KAPNMIILTN YVL GYYNDP AYLVEDISAL DGNDFEYMAH YGKDAFLRRL EFENGPLRDQ VEAHTQKLIA DRAAAAAA

UniProtKB: Letm1 RBD domain-containing protein

+
Macromolecule #6: Mitochondrial ATP synthase subunit ATPTB6

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB6 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 19.162 KDa
SequenceString:
VELTMQYLDE WMLRWRKFQT ESDWQIEKNR QWWRKANIVT AGAVMGGLVM YTAGNATIRR QFGAPHFFDI GDVGKLKEAI CDTMTSRWR YTPQGYGRVM LVGLPTFFVF AISEHIQERR RLRAYVRQNT VFGEQARRLV QNGKIEEYLA VDIKASLPQN Q TQL

UniProtKB: Transmembrane protein

+
Macromolecule #7: Mitochondrial ATP synthase subunit g

MacromoleculeName: Mitochondrial ATP synthase subunit g / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 14.702046 KDa
SequenceString:
MNIAHKIEVH SVKKMQAMEP SMAEWIKAQE AAGADAATIS RQRFLREQRQ LMSYRVVRFF EECRYIASGQ YYKNYNIGCF LQDTRFATQ ALFIFLMAVM VGRRSVYPPI SPNSPLAIAL DHKVNPNY

UniProtKB: Uncharacterized protein

+
Macromolecule #8: Mitochondrial ATP synthase subunit f

MacromoleculeName: Mitochondrial ATP synthase subunit f / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 14.321474 KDa
SequenceString:
FSTYRSKRIV APGFLKGPVM ASRAFFDYYF QRAWCGCVQW VIPGEVRLWA CGVPVIYFIH RYHNDHSLEP DFVEKAMIQR WGGSLEEVR KLSPQDQLRI RAFTDLEKLY SAYGPKDTIV QPPG

UniProtKB: Uncharacterized protein

+
Macromolecule #9: Mitochondrial ATP synthase subunit 8

MacromoleculeName: Mitochondrial ATP synthase subunit 8 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 8.299618 KDa
SequenceString:
EPMSVWYLSS WTCVWWYSFF FWLPVLWADM IVPSFVYNKL PVIHFIQEKR AEQKLRRVLD ETYTQW

UniProtKB: Uncharacterized protein

+
Macromolecule #10: Mitochondrial ATP synthase subunit b

MacromoleculeName: Mitochondrial ATP synthase subunit b / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 9.043121 KDa
SequenceString:
FKDPVRRPQL SPEERAKVKI NYAEWPEEFR DYDPDDPYKN SPEIIEGLSS WNLFLWGVEC AFIYQFYEVV FPKSI

UniProtKB: Uncharacterized protein

+
Macromolecule #11: Mitochondrial ATP synthase subunit e

MacromoleculeName: Mitochondrial ATP synthase subunit e / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 6.960852 KDa
SequenceString:
KTLNQFRNFS YIVVAWLGFN KGFREKAAND AEWIAHQQRV RQQNVERHQA ASAMMEAKQ

UniProtKB: Uncharacterized protein

+
Macromolecule #12: Mitochondrial ATP synthase subunit k

MacromoleculeName: Mitochondrial ATP synthase subunit k / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 12.026902 KDa
SequenceString:
LYHPPKLEDI PPSSATKGFF GAYNGGLAMA RLIDIKWMMN RSVELGREYY ISAPTLYLFL WMFCWKGFVI MRYGDGKPPR HVDWNTEEA GYLPQGFEQT KVTKA

UniProtKB: Uncharacterized protein

+
Macromolecule #13: Mitochondrial ATP synthase subunit ATPTB12

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB12 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 11.454896 KDa
SequenceString:
MSQPLAFHDV STDAIRQMQA SEALQKHLEN AQLAHRVCVA KALKADEPPV EKCALTWGEV VMRYNQWSEY RPAFHDSDAQ KRYSKYWTK KRQAADDSRA

UniProtKB: Uncharacterized protein

+
Macromolecule #14: Mitochondrial ATP synthase subunit ATPTB11

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB11 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 15.722698 KDa
SequenceString:
NGPTFHTAGD NNNTSEIQNA FPINERGIRS SSPFPEPNTA IYDSYMPWTY FQPIDVKVDK MPAPEAKYYQ HHTKKPWDVS TTDLIEIQS RKKYVQGVGY FLMMIYLYFL MPKEKSYSGT TGSDGFYVML PKNQPEK

UniProtKB: Uncharacterized protein

+
Macromolecule #15: Mitochondrial ATP synthase subunit ATPEG3

MacromoleculeName: Mitochondrial ATP synthase subunit ATPEG3 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 10.147562 KDa
SequenceString:
VDHFRPNLKF LSVYVEHQYV VDKWLHVKEN WLKPWYLPWW TPMYQAMTWY SQRNRNLMLV ENHLNYRPYR YRRNDEDR

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
Details: 50 mM HEPES pH 7.9, 300 mM NaCl, 4 mM MgCl2, 20 uM CaCl2, 0.1 mM Dithiothreitol, and 0.5% n-dodecyl-beta-D-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 4649
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: Built de novo using ModelAngelo (v1.014), guided by the cryo-EM density map
Output model

PDB-9zb4:
Cryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) membrane region

+
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