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- EMDB-74030: Cryo-EM structure of Leishmania tarentolae respiratory complex V ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74030
TitleCryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
Map data
Sample
  • Complex: Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
    • Protein or peptide: mitochondrial ATP synthase subunit 8
    • Protein or peptide: mitochondrial ATP synthase subunit ATPTB4
    • Protein or peptide: LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3
    • Protein or peptide: mitochondrial ATP synthase subunit d
KeywordsElectron transport chain / respiratory complex / ATP synthase / mitochondria / ELECTRON TRANSPORT
Function / homologyUncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 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_74030.png

Downloads & links

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Map

FileDownload / File: emd_74030.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0531
Minimum - Maximum-0.051670134 - 0.12239104
Average (Standard dev.)0.0017690609 (±0.007226258)
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_74030_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_74030_additional_1.map
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Half map: #2

Fileemd_74030_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_74030_half_map_2.map
Projections & Slices
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Sample components

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Entire : Leishmania tarentolae respiratory complex V (ATP synthase) periph...

EntireName: Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
Components
  • Complex: Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
    • Protein or peptide: mitochondrial ATP synthase subunit 8
    • Protein or peptide: mitochondrial ATP synthase subunit ATPTB4
    • Protein or peptide: LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3
    • Protein or peptide: mitochondrial ATP synthase subunit d

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Supramolecule #1: Leishmania tarentolae respiratory complex V (ATP synthase) periph...

SupramoleculeName: Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
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)

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Macromolecule #1: mitochondrial ATP synthase subunit 8

MacromoleculeName: mitochondrial ATP synthase subunit 8 / 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: 10.145621 KDa
SequenceString:
EPMSVWYLSS WTCVWWYSFF FWLPVLWADM IVPSFVYNKL PVIHFIQEKR AEQKLRRVLD ETYTQWSTEL EAAHITDAIS RTF

UniProtKB: Uncharacterized protein

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Macromolecule #2: mitochondrial ATP synthase subunit ATPTB4

MacromoleculeName: mitochondrial ATP synthase subunit ATPTB4 / 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: 15.343446 KDa
SequenceString:
SDLKMVSLHK ILIGEVQFRN NALLKACNIE HNFGPTWKSE IEAYAKSLPA EEKNCLERQI ARVSMTRYTT RELAEYCGEG PEHVDAVAR EANIAQAKVY AQKNGADKLE TYVKAEAKNA GWSEAETKKF MDAVKAAK

UniProtKB: Uncharacterized protein

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Macromolecule #3: LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ...

MacromoleculeName: LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 26.703727 KDa
SequenceString: GAPAALLQAV SSILSKATGG AVKATQATSA ASNAVVVGMQ APRGVYACVA EPPSTASGPY AGVKTVVVRA ILPRSAPDTM QVRDILDVY PASGIACEKE TAEAVKNFTK AAKVAVEKAK AMKATRVTLV MKPATKYERL NGLFRETCTK TIEAAGLSVE T STTAAATN ...String:
GAPAALLQAV SSILSKATGG AVKATQATSA ASNAVVVGMQ APRGVYACVA EPPSTASGPY AGVKTVVVRA ILPRSAPDTM QVRDILDVY PASGIACEKE TAEAVKNFTK AAKVAVEKAK AMKATRVTLV MKPATKYERL NGLFRETCTK TIEAAGLSVE T STTAAATN TLIMFPEKMS VVMVSDDPVC ENVQYAYAGA VGGVHTTYYT DSGNKIYGGH SYRSVAMALA EELKSLGMKA EA AKVEAAV QKSPRNAAAA M

UniProtKB: Uncharacterized protein

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Macromolecule #4: mitochondrial ATP synthase subunit d

MacromoleculeName: mitochondrial ATP synthase subunit d / type: protein_or_peptide / ID: 4
Details: Residues 1-29, 169-184, and 324-364 are not modeled due to the absence of density, resulting in breaks between residues 168-185
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 42.279402 KDa
SequenceString: MRRLTPPGLS TQCVRFICGA APVMYFPPVP FASASKEEQI KKNTKIAIEM IRRYKGETPM SYTRKHTATI EQLEREIEAL LGGAQKMRK ATTDDQPMDK LGLMERCLRH ALWSYHKDEG KYDFDEIARW VVYTPEDEVK LAQMKRQVEA KSKLAAYRAK R AEQGLPEA ...String:
MRRLTPPGLS TQCVRFICGA APVMYFPPVP FASASKEEQI KKNTKIAIEM IRRYKGETPM SYTRKHTATI EQLEREIEAL LGGAQKMRK ATTDDQPMDK LGLMERCLRH ALWSYHKDEG KYDFDEIARW VVYTPEDEVK LAQMKRQVEA KSKLAAYRAK R AEQGLPEA PVPQISWEEE YKNVTDRELV NEKRLRYDTI AANTMERDEA QIEAVLQQYR KPIQDKRLDD LVDLLERFKP VL AREAIMQ RLTIKHLEGQ LGVWRYMDWC PEVRDRAELE VDISGFQWWS PLEERRLLPV RLRSVNEVRE IMAQTQSSKA AEA SAHSPQ ASQSAGDGDR ERLLKEVLAL QARIHQRDDA PVEKKAAH

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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 correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9zc4:
Cryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk

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