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- EMDB-73948: Cryo-EM structure of Leishmania tarentolae respiratory complex II... -

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Basic information

Entry
Database: EMDB / ID: EMD-73948
TitleCryo-EM structure of Leishmania tarentolae respiratory complex III (cytochrome bc1 complex)
Map data
Sample
  • Complex: Leishmania tarentolae mitochondria complex III
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
Keywordscytochrome bc1 complex / respiratory complex / complex III / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : ...Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Rieske iron-sulphur protein / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Cytochrome c1, heme protein, mitochondrial, putative / Uncharacterized protein / Mitochondrial processing peptidase alpha subunit, putative / Uncharacterized protein / Ubiquinol-cytochrome-c reductase-like protein / Uncharacterized protein / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex 14 kDa protein / Mitochondrial processing peptide beta subunit, putative / Rieske iron-sulfur protein, putative / Cytochrome b
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 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 18, 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_73948.png

Downloads & links

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Map

FileDownload / File: emd_73948.map.gz / Format: CCP4 / Size: 307.5 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 432 pix.
= 317.952 Å		0.74 Å/pix.
x 432 pix.
= 317.952 Å		0.74 Å/pix.
x 432 pix.
= 317.952 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: 0.0635
Minimum - Maximum-0.1463985 - 0.31568208
Average (Standard dev.)0.00148391 (±0.014381131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 317.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73948_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73948_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73948_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Leishmania tarentolae mitochondria complex III

EntireName: Leishmania tarentolae mitochondria complex III
Components
  • Complex: Leishmania tarentolae mitochondria complex III
    • Protein or peptide: Mitochondrial processing peptidase alpha subunit, putative
    • Protein or peptide: Mitochondrial processing peptide beta subunit, putative
    • Protein or peptide: Ubiquinol-cytochrome c reductase complex 14 kDa protein
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial, putative
    • Protein or peptide: LtaP17.1410, Hypothetical protein, conserved
    • Protein or peptide: LtaP32.3800, Hypothetical protein, conserved
    • Protein or peptide: Rieske iron-sulfur protein, putative
    • Protein or peptide: LtaP35.0250, Hypothetical protein, conserved
    • Protein or peptide: Ubiquinol-cytochrome-c reductase-like protein
    • Protein or peptide: LtaP27.0110, Hypothetical protein, conserved
    • Protein or peptide: unassigned helix
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Leishmania tarentolae mitochondria complex III

SupramoleculeName: Leishmania tarentolae mitochondria complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
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 processing peptidase alpha subunit, putative

MacromoleculeName: Mitochondrial processing peptidase alpha subunit, putative
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: 52.705617 KDa
SequenceString: PSESVPVAAK KVEITKLHNG ARVITHNLGG PSVSVGAYIL AGPAYDPPSA PGAGAMMHLA LTTSNYNNSL FQLDRNIRSV GAAQSHFEK DKHYIGIRID ARADKWKSAA SASSLTQRRQ LQNQKQAEQK FSLNLVQDNI FTCIAAPRFH EPDVERFRDT I DNQVEELR ...String:
PSESVPVAAK KVEITKLHNG ARVITHNLGG PSVSVGAYIL AGPAYDPPSA PGAGAMMHLA LTTSNYNNSL FQLDRNIRSV GAAQSHFEK DKHYIGIRID ARADKWKSAA SASSLTQRRQ LQNQKQAEQK FSLNLVQDNI FTCIAAPRFH EPDVERFRDT I DNQVEELR WQCPAEYAKQ MLETVAFYRE PLGNPRFVPA SSNGIISSSV LLEQYSRYVV PSRVVIAGVN VDHAELIAEY EN TPFPHSA SAPHHAREQP SVPKSKDEAA QYTGGERHDH EDRPKVMGTK PDMDPESIIA VGWLAYGKDK KMVKDHAASM IVK ALMDIQ FSGCVRYAHA EVYEHAGLRA FYSPYQTAGL MGFTAKTEPQ AAVRMVTDAV KMVQAGKAAV ADATLSVAKK MAKM QFMVQ NADTIRDYCD YLGTCLSTDS DSVLATSLEE VVDAIDSVSA ADVKKVYEKM FSNKASLYGH GEMLCFPSLR QMGL

UniProtKB: Mitochondrial processing peptidase alpha subunit, putative

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Macromolecule #2: Mitochondrial processing peptide beta subunit, putative

MacromoleculeName: Mitochondrial processing peptide beta subunit, putative
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 54.669586 KDa
SequenceString: MSVSFSTLVQ RARPASNHAT SAAFREVLSK IPPTNVSTLG NGVRVACEEN PLSKLATVGV WMDAGTRYEP ISYAGTARVL EKCGFLGTT NQSREQIAKA VEELGGQLEV NVGREQTYLY MKVTKENTDR AVGLLADVVR NARMEDADIV KARALVHQDQ H LFEERPDD ...String:
MSVSFSTLVQ RARPASNHAT SAAFREVLSK IPPTNVSTLG NGVRVACEEN PLSKLATVGV WMDAGTRYEP ISYAGTARVL EKCGFLGTT NQSREQIAKA VEELGGQLEV NVGREQTYLY MKVTKENTDR AVGLLADVVR NARMEDADIV KARALVHQDQ H LFEERPDD LVMDNLHRCA FDSTPYGVGT PLYGTEEGVK KVTAEQMRSY RASTLAGNRV IVVGSGGVDH TVLEKAAKSY FG DLPTTPE KAAIVMPESR YVGGEYRLWN LRYKTVNVAW AFETCGAACE DNVPLALACE IPGSFHRSQH ELGQHAMHRV LKT FSSLDH STPTNTHFNE KSIETANPFL HSYKDVGLCG MYVVGRQAMG GPGDGGVIVE VLQYTIAEWC RIAQKMLHDN ELAQ AKVNM KAQLLFNMDG SANSAKDIGR QVLHYGRRVP LTEMYDRIDD TTASNVQEVL QHYFYGRKPV YSYLGYISAI PNYDW TQHW SYKYWY

UniProtKB: Mitochondrial processing peptide beta subunit, putative

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Macromolecule #3: Ubiquinol-cytochrome c reductase complex 14 kDa protein

MacromoleculeName: Ubiquinol-cytochrome c reductase complex 14 kDa protein
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: 23.053461 KDa
SequenceString:
QGIWAGFRYY IGHFFYPNMY REFLSVQNAH KVERALRLQK AIKANKIDYR ALLALPVTDH AHPYKMEYPW EKVMQSDARD LGFYGKWYA SKMMCFYEGL QFHKWGCLQD DLINAHGWWN RAARTRAPKD KIVHGDRRVM RARVLKDKYI YEPRDRWVHP V DNVAYFGP YVMMVADEWE EKWGFFAGQE VEY

UniProtKB: Ubiquinol-cytochrome c reductase complex 14 kDa protein

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Macromolecule #4: Cytochrome b

MacromoleculeName: Cytochrome b / 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: 44.579051 KDa
SequenceString: MFFRVRFLLF FLLFRNLCCL LTSGCLLRVY GVGFSLGFFI CMQIICGVCL AWLFFSCFIC TNWYFVLFLW DFDLGFVIRS THICFTSLL FFLLYVHIFK CIVLIILFDT HILVWAVGFI IYIFIVVIGF IGYVLPCTMM SYWGLTVFSN ILATVPVIGT W LCYWIWGS ...String:
MFFRVRFLLF FLLFRNLCCL LTSGCLLRVY GVGFSLGFFI CMQIICGVCL AWLFFSCFIC TNWYFVLFLW DFDLGFVIRS THICFTSLL FFLLYVHIFK CIVLIILFDT HILVWAVGFI IYIFIVVIGF IGYVLPCTMM SYWGLTVFSN ILATVPVIGT W LCYWIWGS EYINDFTLLK LHVLHVLLPF VLILVIFMHL FCLHYFMSSD GFCDRFAFYC ERLCFCMWFY LRDMFLAFLI LF YVVYFIF INWYFVFHEE SWVIVDTLKT SDKILPEWFF LFLFGFLKAV PDKFTGLLLM VILLFSLFLF ILNCILWFVY CRS SLLWFT YSLILFYSIF MSGFLALYVI LAYPIWMELQ FWVLLLFMLV VCRLD

UniProtKB: Cytochrome b

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Macromolecule #5: Cytochrome c1, heme protein, mitochondrial, putative

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial, putative / 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: 29.907707 KDa
SequenceString: MAGKKAHPIK RDWYWNHNDR LEIWHSLDWP SVRRGRQIYT EVFAPCHSLG RMTFTHFQGF MTREEIKQLA SQYEMIDSEP DAEGNLNRR PGKPTDTLPT PYPNQRAAQF ANNGAEPPDL QHAVFGKEGG SDYIFSLVTG YNWGNGELME IPPFAPEVKP G QFWNPYFK ...String:
MAGKKAHPIK RDWYWNHNDR LEIWHSLDWP SVRRGRQIYT EVFAPCHSLG RMTFTHFQGF MTREEIKQLA SQYEMIDSEP DAEGNLNRR PGKPTDTLPT PYPNQRAAQF ANNGAEPPDL QHAVFGKEGG SDYIFSLVTG YNWGNGELME IPPFAPEVKP G QFWNPYFK GCVLSMPPPL SDGLVDYEDG TPATISQMAK DVVNFLRWSA ESEYDDRRVA FWKVITTVGL VNCLLLHYGQ KN TNWRIYG RTTFRYWKKV W

UniProtKB: Cytochrome c1, heme protein, mitochondrial, putative

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Macromolecule #6: LtaP17.1410, Hypothetical protein, conserved

MacromoleculeName: LtaP17.1410, Hypothetical protein, conserved / 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: 8.021193 KDa
SequenceString:
MAPFWTNVLN YTYARGFIRI PIVLALPIFF NKYVLYEYEG AFKRWNAGHN QVDIWNRLKE KVAADEE

UniProtKB: Uncharacterized protein

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Macromolecule #7: LtaP32.3800, Hypothetical protein, conserved

MacromoleculeName: LtaP32.3800, Hypothetical protein, conserved / 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: 16.839662 KDa
SequenceString:
MAPPKASFPA RIFAGDFMGI NWNRVSWMAP YNNFYPITMC GGWGGRMWSS FIQYGRFDNR AGLIVVRNLI MGIPSALMAL LMLGNMDWF QCMQCAFYLP GIPIPEWAQN KYAKEMEWYS WNKPGAMAKH HYAGTVSIPG TEKYITEM

UniProtKB: Uncharacterized protein

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Macromolecule #8: Rieske iron-sulfur protein, putative

MacromoleculeName: Rieske iron-sulfur protein, putative / 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: 31.494869 KDa
SequenceString: SLVFKQLEGN APLTKKNKPV NSWSDEFMKP PQSAEMTTKY GRYAKYSDPA LCDVDTSEEV VLNTYPDGAP QGRIEATAGV ALKDYDASM WDEEFFRKHI LKPKLADEVE DRARVTDYAL NSAMLGFVIL MARYAVLPLW YVGQPAMSMV GQMNIEAEVG E LDERQCTT ...String:
SLVFKQLEGN APLTKKNKPV NSWSDEFMKP PQSAEMTTKY GRYAKYSDPA LCDVDTSEEV VLNTYPDGAP QGRIEATAGV ALKDYDASM WDEEFFRKHI LKPKLADEVE DRARVTDYAL NSAMLGFVIL MARYAVLPLW YVGQPAMSMV GQMNIEAEVG E LDERQCTT VVWRGKPVFV YRRSARQMKE VTETPLSALK DPETDEARFP DHRDKAVVIA ICTHLGCVPI PNEGLFNGFF CP CHGSHYD PSGRIRQGPA PLNLEVPPYR WIDDNTIYMG KL

UniProtKB: Rieske iron-sulfur protein, putative

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Macromolecule #9: LtaP35.0250, Hypothetical protein, conserved

MacromoleculeName: LtaP35.0250, Hypothetical protein, conserved / 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: 12.990755 KDa
SequenceString:
RAPARPGPTL YGWGRTEQKR RLEYEATESK YHKRDFNKSW DVAGVEQRYS DFMQVRTYFS IGSRWGTWLY NMIQFYVLSM LPIFAFMHF LHKSIEAYDD SIRKAAWW

UniProtKB: Uncharacterized protein

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Macromolecule #10: Ubiquinol-cytochrome-c reductase-like protein

MacromoleculeName: Ubiquinol-cytochrome-c reductase-like protein / 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: 7.981286 KDa
SequenceString:
MASDPVDIKL DLEKECLATD CAKKVEAYNA CLERIKTVSP EKEPHCYNQY FAIVHCVDVC VDPKLWPTLK

UniProtKB: Ubiquinol-cytochrome-c reductase-like protein

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Macromolecule #11: LtaP27.0110, Hypothetical protein, conserved

MacromoleculeName: LtaP27.0110, Hypothetical protein, conserved / 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: 7.997269 KDa
SequenceString:
QSMTAPIGKG SVVPMKFDSL KPAYVPKSFT TQFFVLGTWS ISNMITNFVI GFLIIAAANG GLSGAWPPDP HSLHP

UniProtKB: Uncharacterized protein

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Macromolecule #12: unassigned helix

MacromoleculeName: unassigned helix / 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: 2.060531 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #13: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 13 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 13544
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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