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- EMDB-22448: Plant Mitochondrial complex SC III2+IV from Vigna radiata composi... -

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Basic information

Entry
Database: EMDB / ID: EMD-22448
TitlePlant Mitochondrial complex SC III2+IV from Vigna radiata composite map
Map dataPlant mitochondrial supercomplex III2 IV from Vigna radiata. Composite map.
Sample
  • Complex: Mitochondrial Respiratory Complex III2
    • Protein or peptide: x 20 types
  • Ligand: x 11 types
Keywordsmitochondria / respiration / bioenergetics / plants / OXIDOREDUCTASE
Function / homology
Function and homology information


mitochondrial processing peptidase / respiratory chain complex IV / mitochondrial envelope / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport ...mitochondrial processing peptidase / respiratory chain complex IV / mitochondrial envelope / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / enzyme regulator activity / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : ...Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 / Cytochrome c/quinol oxidase subunit II / Cytochrome b-c1 complex subunit 9 / 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 C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / 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 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106757297 / Complex III subunit 9 / Uncharacterized protein LOC106759053 / mitochondrial processing peptidase / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 5b-2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6a, mitochondrial ...Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106757297 / Complex III subunit 9 / Uncharacterized protein LOC106759053 / mitochondrial processing peptidase / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 5b-2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6a, mitochondrial / Cytochrome c oxidase subunit 5C / Uncharacterized protein LOC106772338 / Complex III subunit II / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 6b-1 / Cytochrome c1-2, heme protein, mitochondrial
Similarity search - Component
Biological speciesVigna radiata (mung bean) / Vigna radiata var. radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMaldonado M / Letts JA
CitationJournal: Elife / Year: 2021
Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants.
Authors: Maria Maldonado / Fei Guo / James A Letts /
Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
History
DepositionAug 12, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jrp
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22448.png

Downloads & links

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Map

FileDownload / File: emd_22448.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlant mitochondrial supercomplex III2 IV from Vigna radiata. Composite map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-36.912239999999997 - 45.661976000000003
Average (Standard dev.)0.00015192044 (±1.1589029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.5984 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.833199218750.833199218750.83319921875
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z426.598426.598426.598
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-36.91245.6620.000

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Supplemental data

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Sample components

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Entire : Mitochondrial Respiratory Complex III2

EntireName: Mitochondrial Respiratory Complex III2
Components
  • Complex: Mitochondrial Respiratory Complex III2
    • Protein or peptide: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
    • Protein or peptide: Alpha-MPP
    • Protein or peptide: COB
    • Protein or peptide: cytochrome c1-2, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 6
    • Protein or peptide: cytochrome b-c1 complex subunit 9
    • Protein or peptide: QCR10
    • Protein or peptide: COX1
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: COX3
    • Protein or peptide: COX4
    • Protein or peptide: cytochrome c oxidase subunit 5b-2, mitochondrial
    • Protein or peptide: cytochrome c oxidase subunit 6a, mitochondrial
    • Protein or peptide: cytochrome c oxidase subunit 6b-1
    • Protein or peptide: Cytochrome c oxidase subunit 5C
    • Protein or peptide: COX7a
    • Protein or peptide: COX7c
  • Ligand: ZINC ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME C
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: LYSINE

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Supramolecule #1: Mitochondrial Respiratory Complex III2

SupramoleculeName: Mitochondrial Respiratory Complex III2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Vigna radiata (mung bean) / Tissue: hypocotyl / Organelle: mitochondria
Molecular weightTheoretical: 485 KDa

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Macromolecule #1: Mitochondrial-processing peptidase subunit beta, mitochondrial is...

MacromoleculeName: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 58.711238 KDa
SequenceString: MSLNRLLSAA RRSDRRASAL SSFRSLSASP ALAPSAASPP APPPPTAMIY DRAAEAIKSK LRQLENPDPR FLKHGNPRPA LSDHTRILA APETRVTTLP NGLRVATESS LAARTATVGV WIDAGSRFET EETNGTAHFL EHMIFKGTER RNARELEEEI E NMGGHLNA ...String:
MSLNRLLSAA RRSDRRASAL SSFRSLSASP ALAPSAASPP APPPPTAMIY DRAAEAIKSK LRQLENPDPR FLKHGNPRPA LSDHTRILA APETRVTTLP NGLRVATESS LAARTATVGV WIDAGSRFET EETNGTAHFL EHMIFKGTER RNARELEEEI E NMGGHLNA YTSREQTTYY AKVTDSDVPQ ALDILADILQ NSRFEENRIS RERDVILREM EEVEGQTEEV IFDHLHATAF QY TPLGRTI LGPAQNIKTI TKAHLQSYIQ THYTAPRMVI AASGAVKHED IVEQVKKLFT KLSTDATTTA QLVAKEPAIF TGS EVRMLD DDIPLAQFAV AFEGASWKDP DSIALMVMQA MLGSWNKTAG GGKHMGSELA QRVGINEVAE SIMAFNTNYK DTGL FGVYA VAKPDCLDDL SYAIMQETTK LVYRVSEDDV TRACNQLKSS LLLHIDGTSP VAEDIGRQLL TYGRRIPFAE LFARI DAVD ASTIKRVANR FIYDKDVAIA AMGPIQRLPD YNWFRRRTYW NRY

UniProtKB: mitochondrial processing peptidase

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Macromolecule #2: Alpha-MPP

MacromoleculeName: Alpha-MPP / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 54.537684 KDa
SequenceString: MYRAAASSFR RHLKGHGSKL GSTRSSTSAA VAARTSKGGL FSWLTGERSS SLPSLDIPLG GVVLPDPLPD SVEQSKTKIT TLSNGLKIA SETSPNPAAS IGLYLDCGSI YETPFSSGAS HLLERMAFKS TTNRSHFRIV REVEAIGGNI GASASREQMG Y TFDALKTY ...String:
MYRAAASSFR RHLKGHGSKL GSTRSSTSAA VAARTSKGGL FSWLTGERSS SLPSLDIPLG GVVLPDPLPD SVEQSKTKIT TLSNGLKIA SETSPNPAAS IGLYLDCGSI YETPFSSGAS HLLERMAFKS TTNRSHFRIV REVEAIGGNI GASASREQMG Y TFDALKTY VPQMVELLVD CVRNPAFLDW EVNEELRKVK AELGELSNNP QGLLLEAIHS AGYSGALAYP LLAPEAALNR LD GPSLEEF VAENYTAPRM VLAAAGVEHE ELVSIAEPLL SDLPNVPRPD EPKSVYVGGD FRRHGESGGT HVALAFEVPG GWH KEKDAI VLTVLQMLMG GGGSFSAGGP GKGMHSRLYL RVLNEYQQIQ SFSAFNSIFN NTGLFGIYAS TSPDFAPKAV DIAA KELIA IASPGQVTQV QLDRAKKSTK SAVLMNLESR MIASEDIGRQ ILTYGERKPL EQFLKAVDEI TLNDITKISQ KIISS PLTM ASYGDVLSVP SYESVNRKFH AK

UniProtKB: Complex III subunit II

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Macromolecule #3: COB

MacromoleculeName: COB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
Molecular weightTheoretical: 44.353543 KDa
SequenceString: MTIRNQRFSL LKEPISSTLN QHLIDYPTPS NLSYWWGFGS LAGICLVIQI VTGVFLAMHY TPHVDLAFNS VEHVMRDVEG GWLLRYMHA NGASMFFIVV YLHIFRGLYY ASYSSPREFV WCLGVVIFLL MIVTAFTGYV LPWGQMSFWG ATVITSLASA I PVVGDTIV ...String:
MTIRNQRFSL LKEPISSTLN QHLIDYPTPS NLSYWWGFGS LAGICLVIQI VTGVFLAMHY TPHVDLAFNS VEHVMRDVEG GWLLRYMHA NGASMFFIVV YLHIFRGLYY ASYSSPREFV WCLGVVIFLL MIVTAFTGYV LPWGQMSFWG ATVITSLASA I PVVGDTIV TWLWGGFSVD NATLNRFFSL HYLLPFLLVG ASLLHLAALH QYGSNNPLGV HSEMDQISFY PYFYVKDLVG WV AFAIFFS IWIFYAPNVL GHPDNYIPAN PMSTPPHIVP EWYFLPIYAI LRSIPDKSGG VAAIALVFIC LLALPFFKSM YVR SSSFRP IYQGIFWLLL ADCLLLGWIG CQPVEAPFVT IGQISSFVFF LFFAITPILG RVGRGIPNSY TTDETEM

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Macromolecule #4: cytochrome c1-2, heme protein, mitochondrial

MacromoleculeName: cytochrome c1-2, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 33.556188 KDa
SequenceString: MTGGVFQLLR RKLHPQFTNS SLLSPIIAKK DGAGSTGSRS LKVLALIGAG VSGFFSFSTV AVADEAEHGL ACPSYPWPHK GILSSYDHA SIRRGHQVYT EVCASCHSMS LISYRDLVGV AYTEEEVKAM AAEIEVVDGP NDEGEMFTRP GKLSDRFPQP Y ANEAAARF ...String:
MTGGVFQLLR RKLHPQFTNS SLLSPIIAKK DGAGSTGSRS LKVLALIGAG VSGFFSFSTV AVADEAEHGL ACPSYPWPHK GILSSYDHA SIRRGHQVYT EVCASCHSMS LISYRDLVGV AYTEEEVKAM AAEIEVVDGP NDEGEMFTRP GKLSDRFPQP Y ANEAAARF ANGGAYPPDL SLITKARHNG QNYVFSLLTG YRDPPAGVSI REGLHYNPYF PGGAIAMPKM LNDGAVEYED GT PATEAQM GKDVVSFLSW AAEPEMEERK LMGFKWIFVL SLALLQAAYY RRLRWSVLKS RKLVLDVVN

UniProtKB: Cytochrome c1-2, heme protein, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 30.051432 KDa
SequenceString: MLRVAAKRLS SLSSSAWRAN HAASAVLSRN PVAPSLSTEE HRSDPFSLRP EFFLPIRGYA TDSLFHPKEN SLIPEIPATV AAVKNPSSK IIYDEHNHER FPPGDPSKRA FAYFVLTGGR FVYASLIRLL VLKFVLSMSA SKDVLALASL EVDLSSIEPG T TVTVKWRG ...String:
MLRVAAKRLS SLSSSAWRAN HAASAVLSRN PVAPSLSTEE HRSDPFSLRP EFFLPIRGYA TDSLFHPKEN SLIPEIPATV AAVKNPSSK IIYDEHNHER FPPGDPSKRA FAYFVLTGGR FVYASLIRLL VLKFVLSMSA SKDVLALASL EVDLSSIEPG T TVTVKWRG KPVFIRRRTE DDIKLANSVD VASLRDPQQD AERVKNPEWL IVIGVCTHLG CIPLPNAGDF GGWFCPCHGS HY DISGRIR KGPAPYNLEV PTYTFLEENK LMIG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #6: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 14.392698 KDa
SequenceString:
MASFLQSFLD PKKNWLAAQH MKSLVKRLSK YGLRYDDLYD PYYDLDVKEA LNRLPKEVVD ARHARLKRAI DLSMKHEYLP EDLQAMQTP FRGYLQDMLA LVKRERAERE ALGGLPLYQR SIP

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #7: cytochrome b-c1 complex subunit 8

MacromoleculeName: cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 8.349831 KDa
SequenceString:
MGKQIVPVKS VIYALSPFQQ KVMTGLWKDL PTKIHHKVSE NWISATLLLG PLVGTYAYVQ NYLEKEKLHH RY

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #8: Cytochrome b-c1 complex subunit 6

MacromoleculeName: Cytochrome b-c1 complex subunit 6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 8.117424 KDa
SequenceString:
MADEEPVDQK RYLEESCKPK CVKPLLEYQA CIKRIHGDDS GQKHCTGQYF DYWFCVDKCV APKLFTKLK

UniProtKB: Cytochrome b-c1 complex subunit 6

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Macromolecule #9: cytochrome b-c1 complex subunit 9

MacromoleculeName: cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 8.20342 KDa
SequenceString:
METVARRRGG GIFESLYKVV MRRNSVYVTF VIAGAFLGER AVDYGIHKLW EANNVGKRYE DIPVLGQKLS EE

UniProtKB: Complex III subunit 9

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Macromolecule #10: QCR10

MacromoleculeName: QCR10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
Molecular weightTheoretical: 8.948875 KDa
SequenceString:
MAGLPARLRI QPADVKAAAM WGVAAATGGL YLVQVSILVL PPVKVVFHFY LVSGFRICLD VKDLRTMPCS APRIWRLYIL I

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Macromolecule #11: COX1

MacromoleculeName: COX1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
Molecular weightTheoretical: 57.960559 KDa
SequenceString: MTNPVRWLFS TNHKDIGTLY FIFGAIAGVM GTCFSVLIRM ELARPGDQIL GGNHQLYNVL ITAHAFLMIF FMVMPAMIGG FGNWFVPIL IGAPDMAFPR LNNISFWLLP PSLLLLLSSA LVEVGSGTGW TVYPPLSGIT SHSGGAVDLA IFSLHLSGVS S ILGSINFI ...String:
MTNPVRWLFS TNHKDIGTLY FIFGAIAGVM GTCFSVLIRM ELARPGDQIL GGNHQLYNVL ITAHAFLMIF FMVMPAMIGG FGNWFVPIL IGAPDMAFPR LNNISFWLLP PSLLLLLSSA LVEVGSGTGW TVYPPLSGIT SHSGGAVDLA IFSLHLSGVS S ILGSINFI TTIFNMRGPG MTMHRSPLFV WSVLVTAFLL LLSLPVLAGA ITMLLTDRNF NTTFFDPAGG GDPILYQHLF WF FGHPEVY ILILPGFGII SHIVSTFSGK PVFGYLGMVY AMISIGVLGF LVWAHHMFTV GLDVDTRAYF TAATMIIAVP TGI KIFSWI ATMWGGSIQY KTPMLFAVGF IFLFTIGGLT GIVLANSGLD IALHDTYYVV AHFHYVLSMG AVFALFAGFY YWVG KIFGR TYPETLGQIH FWITFFGVNL TFFPMHFLGL SGMPRRIPDY PDAYAGWNAL SSFGSYISVV GICCFFVVVT ITSTS GNNI TRANIPWAVE QNSTTLEWLV QSPPAFHTFG ELPAIKETKS YVK

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Macromolecule #12: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 28.391602 KDa
SequenceString: MCGGFPAISF CDAPEPWQLG FQDAATPIMQ GIMDLHHDIF FFLVQIAVFV LWVLSRALWC FRSKISPIPQ RIVHGTTIEI LWTIFPSII LMFIAIPSFT LLYSMDDVVV DPAITIKAIG HQWYWSYEYS DYNNSDEQSL AFDSYMVPED DLELGQLRLL E VDNRVVVP ...String:
MCGGFPAISF CDAPEPWQLG FQDAATPIMQ GIMDLHHDIF FFLVQIAVFV LWVLSRALWC FRSKISPIPQ RIVHGTTIEI LWTIFPSII LMFIAIPSFT LLYSMDDVVV DPAITIKAIG HQWYWSYEYS DYNNSDEQSL AFDSYMVPED DLELGQLRLL E VDNRVVVP AKTHLRVLIT SADVLHSWAV PSLGVKCDAV PGRLNQISTF IQREGVYYGQ CSEICGTNHA FMPIVVEAVS TK DYGSWVS NQIQ

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #13: COX3

MacromoleculeName: COX3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata (mung bean)
Molecular weightTheoretical: 29.967893 KDa
SequenceString: MIESQRHSYH LVDPSPWPIS GSLGALATTV GGVMYMHSFQ GGATLLSLGL IFILYTMFVW WRDVLRESTL EGHHTKVVQL GLRYGFILF IVSEVMFLFA FFWAFFHSSL APTVEIGGIW PPLGIWVLDP WEIPFLNTLI LLSSGAAVTW AHHAILAGKE K RAVYALVA ...String:
MIESQRHSYH LVDPSPWPIS GSLGALATTV GGVMYMHSFQ GGATLLSLGL IFILYTMFVW WRDVLRESTL EGHHTKVVQL GLRYGFILF IVSEVMFLFA FFWAFFHSSL APTVEIGGIW PPLGIWVLDP WEIPFLNTLI LLSSGAAVTW AHHAILAGKE K RAVYALVA TVLLALVFTG FQGMEYYQAP FTISDSIYGS TFFLATGFHG FHVIIGTLFL IICGIRQYLG HLTKEHHVGF EA AAWYWHF VDVVWLFLFV SIYWWGGI

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Macromolecule #14: COX4

MacromoleculeName: COX4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 8.81102 KDa
SequenceString:
MSTKYIVSAI LGSFGIAWVC DYYVSEKKIF GGSTPGTITN KEWGEETDKK FQAWPRTAGP PVVVNPITRQ NFVVKSRSE

UniProtKB: Uncharacterized protein LOC106757297

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Macromolecule #15: cytochrome c oxidase subunit 5b-2, mitochondrial

MacromoleculeName: cytochrome c oxidase subunit 5b-2, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 16.694705 KDa
SequenceString:
MLRRFLSHSN LRSLHTALSP SRPRFAAPLL TRHVTAQSGA SSVRKRVEDV VPIATGHERE EIQASLEGRD ILEINHPEGP FGTKEAPAI VKSYFDRRIV GCPGGEGEDE HDVVWFWLEN GKPHECPVCS QYFELKVVGP GGDPYGHGDH H

UniProtKB: Cytochrome c oxidase subunit 5b-2, mitochondrial

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Macromolecule #16: cytochrome c oxidase subunit 6a, mitochondrial

MacromoleculeName: cytochrome c oxidase subunit 6a, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 11.225671 KDa
SequenceString:
MATSLVRSGF LRTALRGGAR GSQVPKRNFS SAGHHDDAYE TAKWEKITYL GIVSCTGLAI YNLSKGHPHT EEPPAYPYLH IRNKEFPWG PDGLFETKKH H

UniProtKB: Cytochrome c oxidase subunit 6a, mitochondrial

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Macromolecule #17: cytochrome c oxidase subunit 6b-1

MacromoleculeName: cytochrome c oxidase subunit 6b-1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 20.018635 KDa
SequenceString:
MAETAANKSQ SLAEEYHVSD KQEKTAVVEK PVEVKEVENP QEAGSVEAVV EKIVEETTPV APAVAQESSE VSPPPAEESA EESTEEQSS GNVEDNSGNE DAAEKTPEIK LETAPADFRF PTTNQTRHCF TRYIEYHRCV AAKGEGASEC DKFAKYYRSL C PGEWIDRW NEQRENGTFP GPL

UniProtKB: Cytochrome c oxidase subunit 6b-1

+
Macromolecule #18: Cytochrome c oxidase subunit 5C

MacromoleculeName: Cytochrome c oxidase subunit 5C / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 7.120326 KDa
SequenceString:
MAGPRIAHAT LKGPSVVKEI IIGITLGLAA GSVWKMHHWN EQRKIRTFYD LLEKGEIGVV VDEQ

UniProtKB: Cytochrome c oxidase subunit 5C

+
Macromolecule #19: COX7a

MacromoleculeName: COX7a / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 7.622931 KDa
SequenceString:
MSEPPFRPRE KLIEKQKHFQ SVHKHTYLKG PYDKITSVAI PLALAASSLY LIGRGIYNMS HGIGKKE

UniProtKB: Uncharacterized protein LOC106759053

+
Macromolecule #20: COX7c

MacromoleculeName: COX7c / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vigna radiata var. radiata (mung bean)
Molecular weightTheoretical: 10.505158 KDa
SequenceString:
MAFNNALRSA AKLIASSESS ISTSVSRGFH STPMKRMGGG HGHDEPYYIH AKHMYNLDRM KHRGLKMSLA VFSAFSIGVA VPVYAVIFQ QKKTASA

UniProtKB: Uncharacterized protein LOC106772338

+
Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #22: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 22 / Number of copies: 5 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

+
Macromolecule #23: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 23 / Number of copies: 9 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 24 / 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 #25: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 25 / Number of copies: 29 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

+
Macromolecule #26: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 26 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #27: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 27 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #28: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 28 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #29: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 29 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #30: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

+
Macromolecule #31: LYSINE

MacromoleculeName: LYSINE / type: ligand / ID: 31 / Number of copies: 1 / Formula: LYS
Molecular weightTheoretical: 147.195 Da
Chemical component information

ChemComp-LYS:
LYSINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaCl
1.0 mMEDTA
0.2 %digitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III
DetailsThis sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 60010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 150000000
Startup modelType of model: NONE / Details: Ab initio model generation
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29348
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: Stochastic gradient descent
Final angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: Stochastic gradient descent

-
Atomic model buiding 1

Initial model
PDB IDChain

6q9e

source_name: PDB, initial_model_type: experimental model

6hu9

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 67 / Target criteria: correlation coefficient
Output model

PDB-7jrp:
Plant Mitochondrial complex SC III2+IV from Vigna radiata

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