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- EMDB-74031: Cryo-EM structure of Leishmania tarentolae respiratory complex V ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74031
TitleCryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) Fo monomer membrane region
Map data
Sample
  • Complex: Fo monomer membrane region of Leishmania tarentolae respiratory complex V (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: 3.62 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 22, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74031.png

Downloads & links

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Map

FileDownload / File: emd_74031.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 480 pix.
= 353.28 Å		0.74 Å/pix.
x 480 pix.
= 353.28 Å		0.74 Å/pix.
x 480 pix.
= 353.28 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: 0.0673
Minimum - Maximum-0.086111896 - 0.17336681
Average (Standard dev.)0.0018015188 (±0.009592907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74031_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_74031_additional_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74031_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74031_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Fo monomer membrane region of Leishmania tarentolae respiratory c...

EntireName: Fo monomer membrane region of Leishmania tarentolae respiratory complex V (ATP synthase)
Components
  • Complex: Fo monomer membrane region of Leishmania tarentolae respiratory complex V (ATP synthase)
    • Protein or peptide: Mitochondrial ATP synthase subunit e
    • Protein or peptide: LtATPEG4, LtaP27:632926-633111
    • 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 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

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Supramolecule #1: Fo monomer membrane region of Leishmania tarentolae respiratory c...

SupramoleculeName: Fo monomer membrane region of Leishmania tarentolae respiratory complex V (ATP synthase)
type: complex / ID: 1 / Parent: 0
Macromolecule list: #13, #15, #3, #12, #2, #4, #8-#9, #5, #10-#11, #7, #1, #6, #14
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)

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Macromolecule #1: Mitochondrial ATP synthase subunit ATPTB12

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

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Macromolecule #2: Mitochondrial ATP synthase subunit i/j

MacromoleculeName: Mitochondrial ATP synthase subunit i/j / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

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Macromolecule #3: Mitochondrial ATP synthase subunit c-1

MacromoleculeName: Mitochondrial ATP synthase subunit c-1 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / 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

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Macromolecule #4: Mitochondrial ATP synthase subunit ATPTB1

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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

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Macromolecule #5: Mitochondrial ATP synthase subunit f

MacromoleculeName: Mitochondrial ATP synthase subunit f / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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

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Macromolecule #6: Mitochondrial ATP synthase subunit ATPTB11

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / 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

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Macromolecule #7: Mitochondrial ATP synthase subunit k

MacromoleculeName: Mitochondrial ATP synthase subunit k / type: protein_or_peptide / ID: 7 / Number of copies: 1 / 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

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Macromolecule #8: Mitochondrial ATP synthase subunit ATPTB6

MacromoleculeName: Mitochondrial ATP synthase subunit ATPTB6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / 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 GVDGKLKEAI CDTMTSRWR YTPQGYGRVM LVGLPTFFVF AISEHIQERR RLRAYVRQNT VFGEQARRLV QNGKIEEYLA VDIKASLPQN Q TQL

UniProtKB: Transmembrane protein

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Macromolecule #9: Mitochondrial ATP synthase subunit g

MacromoleculeName: Mitochondrial ATP synthase subunit g / type: protein_or_peptide / ID: 9 / Number of copies: 1 / 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

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Macromolecule #10: Mitochondrial ATP synthase subunit 8

MacromoleculeName: Mitochondrial ATP synthase subunit 8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / 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

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Macromolecule #11: Mitochondrial ATP synthase subunit b

MacromoleculeName: Mitochondrial ATP synthase subunit b / type: protein_or_peptide / ID: 11 / Number of copies: 1 / 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

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Macromolecule #12: ATPase 6

MacromoleculeName: ATPase 6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / 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

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Macromolecule #13: Mitochondrial ATP synthase subunit e

MacromoleculeName: Mitochondrial ATP synthase subunit e / type: protein_or_peptide / ID: 13 / Number of copies: 1 / 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

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Macromolecule #14: Mitochondrial ATP synthase subunit ATPEG3

MacromoleculeName: Mitochondrial ATP synthase subunit ATPEG3 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / 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

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Macromolecule #15: LtATPEG4, LtaP27:632926-633111

MacromoleculeName: LtATPEG4, LtaP27:632926-633111 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 8358
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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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
SoftwareName: Coot (ver. 0.9.6)
Output model

PDB-9zc5:
Cryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) Fo monomer membrane region

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