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- EMDB-45567: Human kidney respiratory complex III -

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Basic information

Entry
Database: EMDB / ID: EMD-45567
TitleHuman kidney respiratory complex III
Map data
Sample
  • Complex: respiratory complex III
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
Keywordshuman / kidney / respiratory complex III / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly / response to D-galactosamine / Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly ...Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly / response to D-galactosamine / Complex III assembly / Complex III assembly / Complex III assembly / Complex III assembly / response to mercury ion / Respiratory electron transport / subthalamus development / pons development / response to cobalamin / cerebellar Purkinje cell layer development / mitochondrial respiratory chain complex III assembly / pyramidal neuron development / response to alkaloid / cellular respiration / thalamus development / Mitochondrial protein import / respiratory chain complex / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / response to glucagon / quinol-cytochrome-c reductase activity / response to copper ion / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / electron transport coupled proton transport / animal organ regeneration / response to hyperoxia / response to cadmium ion / Mitochondrial protein degradation / aerobic respiration / response to activity / respiratory electron transport chain / generation of precursor metabolites and energy / hippocampus development / response to calcium ion / metalloendopeptidase activity / response to toxic substance / 2 iron, 2 sulfur cluster binding / response to ethanol / response to hypoxia / electron transfer activity / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / nucleus / 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-like domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 10 / Cytochrome b / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsZhang Z / Lyu M / 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: Human kidney respiratory complex III
Authors: Zhang Z / Lyu M
History
DepositionJun 28, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_45567.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.51137906 - 0.94010276
Average (Standard dev.)0.00031960287 (±0.036214188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : respiratory complex III

EntireName: respiratory complex III
Components
  • Complex: respiratory complex III
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: HEME C
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: respiratory complex III

SupramoleculeName: respiratory complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.922376 KDa
SequenceString:
MGREFGNLTR MRHVISYSLS PFEQRAYPHV FTKGIPNVLR RIRESFFRVV PQFVVFYLIY TWGTEEFERS KRKNPAAYEN DK

UniProtKB: Cytochrome b-c1 complex subunit 8

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.704971 KDa
SequenceString: MLSVASRSGP FAPVLSATSR GVAGALRPLV QATVPATPEQ PVLDLKRPFL SRESLSGQAV RRPLVASVGL NVPASVCYSH TDIKVPDFS EYRRLEVLDS TKSSRESSEA RKGFSYLVTG VTTVGVAYAA KNAVTQFVSS MSASADVLAL AKIEIKLSDI P EGKNMAFK ...String:
MLSVASRSGP FAPVLSATSR GVAGALRPLV QATVPATPEQ PVLDLKRPFL SRESLSGQAV RRPLVASVGL NVPASVCYSH TDIKVPDFS EYRRLEVLDS TKSSRESSEA RKGFSYLVTG VTTVGVAYAA KNAVTQFVSS MSASADVLAL AKIEIKLSDI P EGKNMAFK WRGKPLFVRH RTQKEIEQEA AVELSQLRDP QHDLDRVKKP EWVILIGVCT HLGCVPIANA GDFGGYYCPC HG SHYDASG RIRLGPAPLN LEVPTYEFTS DDMVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #3: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.320495 KDa
SequenceString:
MAAATLTSKL YSLLFRRTST FALTIIVGVM FFERAFDQGA DAIYDHINEG KLWKHIKHKY ENK

UniProtKB: Cytochrome b-c1 complex subunit 9

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Macromolecule #4: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.753787 KDa
SequenceString:
MGLEDEQKML TESGDPEEEE EEEEELVDPL TTVREQCEQL EKCVKARERL ELCDERVSSR SHTEEDCTEE LFDFLHARDH CVAHKLFNN LK

UniProtKB: Cytochrome b-c1 complex subunit 6, mitochondrial

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Macromolecule #5: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.554477 KDa
SequenceString:
MAGKQAVSAS GKWLDGIRKW YYNAAGFNKL GLMRDDTIYE DEDVKEAIRR LPENLYNDRM FRIKRALDLN LKHQILPKEQ WTKYEEENF YLEPYLKEVI RERKEREEWA KK

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #6: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.577658 KDa
SequenceString:
MVTRFLGPRY RELVKNWVPT AYTWGAVGAV GLVWATDWRL ILDWVPYING KFKKDN

UniProtKB: Cytochrome b-c1 complex subunit 10

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Macromolecule #7: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.469 KDa
SequenceString: MAAAAASLRG VVLGPRGAGL PGARARGLLC SARPGQLPLR TPQAVALSSK SGLSRGRKVM LSALGMLAAG GAGLAMALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCASCHSMDF VAYRHLVGVC YTEDEAKELA AEVEVQDGPN E DGEMFMRP ...String:
MAAAAASLRG VVLGPRGAGL PGARARGLLC SARPGQLPLR TPQAVALSSK SGLSRGRKVM LSALGMLAAG GAGLAMALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCASCHSMDF VAYRHLVGVC YTEDEAKELA AEVEVQDGPN E DGEMFMRP GKLFDYFPKP YPNSEAARAA NNGALPPDLS YIVRARHGGE DYVFSLLTGY CEPPTGVSLR EGLYFNPYFP GQ AIAMAPP IYTDVLEFDD GTPATMSQIA KDVCTFLRWA SEPEHDHRKR MGLKMLMMMA LLVPLVYTIK RHKWSVLKSR KLA YRPPK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

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Macromolecule #8: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.745285 KDa
SequenceString: MTPMRKTNPL MKLINHSFID LPTPSNISAW WNFGSLLGAC LILQITTGLF LAMHYSPDAS TAFSSIAHIT RDVNYGWIIR YLHANGASM FFICLFLHIG RGLYYGSFLY SETWNIGIIL LLATMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VQWIWGGY ...String:
MTPMRKTNPL MKLINHSFID LPTPSNISAW WNFGSLLGAC LILQITTGLF LAMHYSPDAS TAFSSIAHIT RDVNYGWIIR YLHANGASM FFICLFLHIG RGLYYGSFLY SETWNIGIIL LLATMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VQWIWGGY SVDSPTLTRF FTFHFILPFI IAALATLHLL FLHETGSNNP LGITSHSDKI TFHPYYTIKD ALGLLLFLLS LM TLTLFSP DLLGDPDNYT LANPLNTPPH IKPEWYFLFA YTILRSVPNK LGGVLALLLS ILILAMIPIL HMSKQQSMMF RPL SQSLYW LLAADLLILT WIGGQPVSYP FTIIGQVASV LYFTTILILM PTISLIENKM LKWA

UniProtKB: Cytochrome b

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Macromolecule #9: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.495809 KDa
SequenceString: MKLLTRAGSF SRFYSLKVAP KVKATAAPAG APPQPQDLEF TKLPNGLVIA SLENYSPVSR IGLFIKAGSR YEDFSNLGTT HLLRLTSSL TTKGASSFKI TRGIEAVGGK LSVTATRENM AYTVECLRGD VDILMEFLLN VTTAPEFRRW EVADLQPQLK I DKAVAFQN ...String:
MKLLTRAGSF SRFYSLKVAP KVKATAAPAG APPQPQDLEF TKLPNGLVIA SLENYSPVSR IGLFIKAGSR YEDFSNLGTT HLLRLTSSL TTKGASSFKI TRGIEAVGGK LSVTATRENM AYTVECLRGD VDILMEFLLN VTTAPEFRRW EVADLQPQLK I DKAVAFQN PQTHVIENLH AAAYRNALAN PLYCPDYRIG KVTSEELHYF VQNHFTSARM ALIGLGVSHP VLKQVAEQFL NM RGGLGLS GAKANYRGGE IREQNGDSLV HAAFVAESAV AGSAEANAFS VLQHVLGAGP HVKRGSNTTS HLHQAVAKAT QQP FDVSAF NASYSDSGLF GIYTISQATA AGDVIKAAYN QVKTIAQGNL SNTDVQAAKN KLKAGYLMSV ESSECFLEEV GSQA LVAGS YMPPSTVLQQ IDSVANADII NAAKKFVSGQ KSMAASGNLG HTPFVDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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Macromolecule #10: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.704652 KDa
SequenceString: MAASVVCRAA TAGAQVLLRA RRSPALLRTP ALRSTATFAQ ALQFVPETQV SLLDNGLRVA SEQSSQPTCT VGVWIDVGSR FETEKNNGA GYFLEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLGD IVQNCSLEDS Q IEKERDVI ...String:
MAASVVCRAA TAGAQVLLRA RRSPALLRTP ALRSTATFAQ ALQFVPETQV SLLDNGLRVA SEQSSQPTCT VGVWIDVGSR FETEKNNGA GYFLEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLGD IVQNCSLEDS Q IEKERDVI LREMQENDAS MRDVVFNYLH ATAFQGTPLA QAVEGPSENV RKLSRADLTE YLSTHYKAPR MVLAAAGGVE HQ QLLDLAQ KHLGGIPWTY AEDAVPTLTP CRFTGSEIRH RDDALPFAHV AIAVEGPGWA SPDNVALQVA NAIIGHYDCT YGG GVHLSS PLASGAVANK LCQSFQTFSI CYAETGLLGA HFVCDRMKID DMMFVLQGQW MRLCTSATES EVARGKNILR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIAE VDASVVREIC SKYIYDQCPA VAGYGPIEQL PDYNRIRSGM FWLRF

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

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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: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 12 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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: 7.5
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: 38.0 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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11523
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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