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- EMDB-45282: Cryo-EM structure of respiratory supercomplex III -

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Basic information

Entry
Database: EMDB / ID: EMD-45282
TitleCryo-EM structure of respiratory supercomplex III
Map data
Sample
  • Complex: Cryo-EM structure of respiratory supercomplex III
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
Keywordselectron transporter / heart / respiratory supercomplex / ELECTRON TRANSPORT
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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 / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / 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 family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 7 / Cytochrome c1 / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 8 / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome b
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsZhang Z / Maharjan R / Tringides M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of respiratory supercomplex III
Authors: Zhang Z / Maharjan R / Tringides M
History
DepositionJun 10, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45282.png

Downloads & links

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Map

FileDownload / File: emd_45282.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.71715623 - 1.4083031
Average (Standard dev.)-0.00065852614 (±0.031390432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45282_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_45282_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of respiratory supercomplex III

EntireName: Cryo-EM structure of respiratory supercomplex III
Components
  • Complex: Cryo-EM structure of respiratory supercomplex III
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
    • Protein or peptide: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C

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Supramolecule #1: Cryo-EM structure of respiratory supercomplex III

SupramoleculeName: Cryo-EM structure of respiratory supercomplex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 10.685803 KDa
SequenceString:
MGLEDEQRML TGSGDPKEEE EEEEELVDPL TTVREQCEQI EKCIKARERL ELCDQRVSSR SQTEEDCTEE LFDFLHARDH CVAHKLFNS LK

UniProtKB: Cytochrome b-c1 complex subunit 6

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Macromolecule #2: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein

MacromoleculeName: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.41253 KDa
SequenceString:
MAAPTLTARL YSLLFRRTST FALTIAVGAL FFERAFDQGA DAIYEHINQG KLWKHIKHKY ENKE

UniProtKB: Complex III subunit 9

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Macromolecule #3: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1

MacromoleculeName: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 32.174654 KDa
SequenceString: SSAGALTSRI PRLSPLYAPA PLAEGRPGDP PGFQSCCRHV VCRFPLGPFC AGVVGHAALP ATSESPVLDA KRSFLCRESL SGQAAGRPL VASVGLNVPA SVRYSHTDIR VPDFSDYRRA EVLDSTKSSK ESSDARKGFS YLITATTTVG VAYAAKNAVS Q FVSSMSAS ...String:
SSAGALTSRI PRLSPLYAPA PLAEGRPGDP PGFQSCCRHV VCRFPLGPFC AGVVGHAALP ATSESPVLDA KRSFLCRESL SGQAAGRPL VASVGLNVPA SVRYSHTDIR VPDFSDYRRA EVLDSTKSSK ESSDARKGFS YLITATTTVG VAYAAKNAVS Q FVSSMSAS ADVLAMSKIE IKLSDIPEGK NMAFKWRGKP LFVRHRTKKE IDQEAAVEVS QLRDPQHDLE RVKKPEWVIL IG VCTHLGC VPIANAGDFG GYYCPCHGSH YDASGRIRKG PAPLNLEVPT YEFTSDDLVI VG

UniProtKB: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1

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Macromolecule #4: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.560654 KDa
SequenceString:
MLSRFLGPRY RELARNWIPT ASMWGAVGAV GLVWATDWRL ILDWVPYING KFKKED

UniProtKB: Cytochrome b-c1 complex subunit 10

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Macromolecule #5: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 52.75632 KDa
SequenceString: MAASAVCRVA GTGSRVLLRT CRSPALLRSP ALRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YENEKNNGA GYFVEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI ...String:
MAASAVCRVA GTGSRVLLRT CRSPALLRSP ALRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YENEKNNGA GYFVEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI LQELQENDSS MRDVVFDYLH ATAFQGTPLA QSVEGPSENV RKLSRADLTE YVSQHYKAPR MVLAAAGGVE HR QLLDLAQ KHFSSLSGTY VEDAVPAFTP CRFTGSEIRH RDDALPLAHV AIAVEGPGWA NPDNVPLQVA NAIIGHYDST YGG GTHMSS TLASVAATRK LCQSFQTFNI CYAETGLLGA HFVCDNMSID DMMFFLQGQW MRLCTSATES EVVRGKNILR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIAE VDASVVREVC SKYFYDQCPA VAGLGPIEQL PDYNRIRSGM FWLRF

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

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Macromolecule #6: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 48.262434 KDa
SequenceString: MKLITRAGSF SRFYSLKVAP KALASAAPAG VPLQPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRESM AYTVECLRDD IEILMEFLLN VTAAPEFRRW EVAALQSQLR I DKAVAFQN ...String:
MKLITRAGSF SRFYSLKVAP KALASAAPAG VPLQPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRESM AYTVECLRDD IEILMEFLLN VTAAPEFRRW EVAALQSQLR I DKAVAFQN PQAQVLENLH AAAYRNALAN SLYCPDYRIG KVTPDQLHYY VQNHFTSARM ALIGLGVSHP VLKQVAERFL NM RGGLGLS GAKAKYRGGE IRDQNGDSLV HAALVAESAA TGSAEANAFS VLQHVLGAGP HVKRGSNATS SLYQAVAKGV HQP FDVSAF NASYSDSGLF GIYTISQAAS AGDVIKSAYD QVKTIAQGNL SNTDVQAAKN KLKAGYLMSV ESSEGFLDEV GSQA LVAGS YVQPSTVLQQ IDSVADADVI NAAKKFVSGR KSMAASGNLG HTPFVDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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Macromolecule #7: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.840715 KDa
SequenceString: MTNIRKSHPL MKIINNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWVIR YLHANGASM FFICLFIHVG RGLYYGSYMF LETWNIGVVL LFTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VEWIWGGF ...String:
MTNIRKSHPL MKIINNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWVIR YLHANGASM FFICLFIHVG RGLYYGSYMF LETWNIGVVL LFTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VEWIWGGF SVDKATLTRF FAFHFILPFI ITALAAVHLL FLHETGSNNP TGISSDMDKI PFHPYYTIKD ILGALFMMLI LL ILVLFSP DLLGDPDNYT PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALVAS ILILILMPML HTSKQRSMMF RPL SQCLFW MLVADLITLT WIGGQPVEHP FIIIGQLASI LYFLIILVLM PITSIIENNL LKW

UniProtKB: Cytochrome b

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Macromolecule #8: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 35.48893 KDa
SequenceString: MSAAAAASLR GAVLGPRGAG LPGARARGLL CGPRPGQLPL RTPQALSLSS KSGLSRGRKV ILSALGMLAA GGAGLAVALH SAVSATDLE LHAPSYPWSH RGLLSSLDHT SIRRGFQVYK QVCSSCHSMD YVAYRHLVGV CYTEEEAKAL AEEVEVQDGP N EDGEMFMR ...String:
MSAAAAASLR GAVLGPRGAG LPGARARGLL CGPRPGQLPL RTPQALSLSS KSGLSRGRKV ILSALGMLAA GGAGLAVALH SAVSATDLE LHAPSYPWSH RGLLSSLDHT SIRRGFQVYK QVCSSCHSMD YVAYRHLVGV CYTEEEAKAL AEEVEVQDGP N EDGEMFMR PGKLSDYFPK PYPNPEAARA ANNGALPPDL SYIVRARHGG EDYVFSLLTG YCEPPTGVSL REGLYFNPYF PG QAIAMAP PIYNEVLEFD DGTPATMSQV AKDVCTFLRW ASEPEHDHRK RMGLKMLMMM GLLLPLVYAM KRHKWSVLKS RKL AYRPPK

UniProtKB: Cytochrome c1

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Macromolecule #9: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.587549 KDa
SequenceString:
MASRPAVAAS SKWLEGIRKW YYNAAGFNKL GLMRDDTIYE DDDVKEAIRR LPENLYNDRV FRIKRALDLT MRQQILPKEQ WTKYEEDKF YLEPYLKEVI RERKEREEWA KK

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #10: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.784339 KDa
SequenceString:
MGREFGHLTR MRHVITYSLS PFEQRAFPHY FTKGIPNVLR RTRACILRVA PPFVVFYLVY TWGTQEFEKS KRKNPAAYEN DK

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #11: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 11 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #12: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 12 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #13: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 13 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
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: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43845
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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