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- EMDB-46995: Mycobacterial supercomplex malate:quinone oxidoreductase assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-46995
TitleMycobacterial supercomplex malate:quinone oxidoreductase assembly
Map dataMycobacterium smegmatis supercomplex malate:quinone oxidoreductase assembly, composite map
Sample
  • Complex: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis
    • Protein or peptide: x 13 types
  • Ligand: x 11 types
KeywordsElectron transport chain / mycobacterial CIII2CIV2 supercomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


malate dehydrogenase (quinone) / L-malate dehydrogenase (quinone) activity / 2-hydroxyglutarate dehydrogenase activity / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase ...malate dehydrogenase (quinone) / L-malate dehydrogenase (quinone) activity / 2-hydroxyglutarate dehydrogenase activity / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport / tricarboxylic acid cycle / respiratory electron transport chain / monooxygenase activity / electron transport chain / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Malate:quinone-oxidoreductase / Malate:quinone oxidoreductase (Mqo) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB ...Malate:quinone-oxidoreductase / Malate:quinone oxidoreductase (Mqo) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome c / Rieske iron-sulphur protein / 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 / Cupredoxin / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Cytochrome c oxidase subunit 1 / Probable malate:quinone oxidoreductase / Probable cytochrome c oxidase subunit 3 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 complex cytochrome c subunit / Cytochrome c oxidase polypeptide 4 / Uncharacterized protein / Superoxide dismutase [Cu-Zn] / Cytochrome bc1 complex Rieske iron-sulfur subunit ...Cytochrome c oxidase subunit 1 / Probable malate:quinone oxidoreductase / Probable cytochrome c oxidase subunit 3 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 complex cytochrome c subunit / Cytochrome c oxidase polypeptide 4 / Uncharacterized protein / Superoxide dismutase [Cu-Zn] / Cytochrome bc1 complex Rieske iron-sulfur subunit / cytochrome-c oxidase / LpqE protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDi Trani JM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)JT162186 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and aerobic respiration in mycobacteria.
Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / ...Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / John L Rubinstein /
Abstract: To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged ...To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged the vesicles with electron cryomicroscopy. We show that this analysis allows determination of the structure of both mycobacterial ATP synthase and the supercomplex of respiratory complexes III and IV in their native membrane. The latter structure reveals that the enzyme malate:quinone oxidoreductase (Mqo) physically associates with the respiratory supercomplex, an interaction that is lost on extraction of the proteins from the lipid bilayer. Mqo catalyzes an essential reaction in the Krebs cycle, and in vivo survival of mycobacterial pathogens is compromised when its activity is absent. We show with high-speed spectroscopy that the Mqo:supercomplex interaction enables rapid electron transfer from malate to the supercomplex. Further, the respiratory supercomplex is necessary for malate-driven, but not NADH-driven, electron transport chain activity and oxygen consumption. Together, these findings indicate a connection between the Krebs cycle and aerobic respiration that directs electrons along a single branch of the mycobacterial electron transport chain.
History
DepositionSep 11, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_46995.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium smegmatis supercomplex malate:quinone oxidoreductase assembly, composite map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.335
Minimum - Maximum-1.5788541 - 2.1295056
Average (Standard dev.)0.002324249 (±0.05799798)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 374.91998 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 Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis

EntireName: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis
Components
  • Complex: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
    • Protein or peptide: Cytochrome aa3 subunit 2
    • Protein or peptide: Cytochrome aa3 subunit 3
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Cytochrome c oxidase subunit CtaJ
    • Protein or peptide: Uncharacterized protein MSMEG_4692/MSMEI_4575
    • Protein or peptide: Conserved transmembrane protein
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: LpqE protein
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
    • Protein or peptide: Probable malate:quinone oxidoreductase
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: MENAQUINONE-9
  • Ligand: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • Ligand: HEME C
  • Ligand: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis

SupramoleculeName: Respiratory Complex Mqo:CIII2CIV2SoD2 from Mycobacterium smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155

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Macromolecule #1: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 63.296922 KDa
SequenceString: ELEARRPFPE RMGPKGNLIY KLITTTDHKL IGIMYCVVCF AFFLVGGLMA LFMRTELAMP GLQFLSNEQF NQLFTMHGTV MLLFYATPI VFGFANLVLP LQIGAPDVAF PRLNALSFWL FLFGALIAIA GFITPGGAAD FGWTAYSPLT DAIHSPGAGG D LWIMGLAV ...String:
ELEARRPFPE RMGPKGNLIY KLITTTDHKL IGIMYCVVCF AFFLVGGLMA LFMRTELAMP GLQFLSNEQF NQLFTMHGTV MLLFYATPI VFGFANLVLP LQIGAPDVAF PRLNALSFWL FLFGALIAIA GFITPGGAAD FGWTAYSPLT DAIHSPGAGG D LWIMGLAV GGLGTILGGV NMITTVVCMR APGMTMFRMP IFTWNILVTS ILVLIAFPIL TAALFGLAAD RHLGAHIYDP AN GGVLLWQ HLFWFFGHPE VYIIALPFFG IVSEIFPVFS RKPIFGYTTL IYATLAIAAL SVAVWAHHMY ATGAVLLPFF SFM TFLIAV PTGIKFFNWI GTMWKGQLTF ETPMLFSVGF LITFLLGGLS GVLLASPPLD FHVTDSYFVI AHFHYVLFGT IVFA TYAGI YFWFPKMTGR LLDERLGKLH FWLTFIGFHT TFLVQHWLGD EGMPRRYADY LPTDGFTTLN VISTVGAFIL GVSML PFVW NVFKSWRYGE PVTVDDPWGY GNSLEWATSC PPPRHNFTEL PRIRSERPAF ELHYPHMVER MRAEAHVGRA HHPELE TAD KSS

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #2: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 59.110758 KDa
SequenceString: DFAKLAAAQG DAIDSRYHPS AAVRRQLNKV FPTHWSFLLG EIALYSFIIL LLTGVWLTLF FDPSMAHVTY DGVYQPLRGV QMSRAYETA LDISFEVRGG LFVRQVHHWA ALMFAASIMV HLARIFFTGA FRRPREANWV IGSLLLILAM FEGFFGYSLP D DLLSGTGI ...String:
DFAKLAAAQG DAIDSRYHPS AAVRRQLNKV FPTHWSFLLG EIALYSFIIL LLTGVWLTLF FDPSMAHVTY DGVYQPLRGV QMSRAYETA LDISFEVRGG LFVRQVHHWA ALMFAASIMV HLARIFFTGA FRRPREANWV IGSLLLILAM FEGFFGYSLP D DLLSGTGI RAALSGITMG IPVIGTWMHW ALFGGDFPGE ILIPRLYALH ILLIPGIILA LIGAHLALVW FQKHTQFPGP GR TETNVVG VRVMPVFAVK SGAFFAMITG VLGLMGGLLT INPIWNLGPY KPSQVSAGSQ PDFYMMWTDG LIRLWPAWEF YPF GHTIPQ GVWVAVGMGL VFALLIAYPF IEKKVTGDDA HHNLLQRPRD VPVRTAIGSM AIALYLLLTF ACMNDIIALK FHIS LNATT WIGRIGMVVL PAIVYFVAYR WAISLQRSDR EVLEHGVETG IIKRLPHGAY VELHQPLGPV DEHGHPIPLE YAGAP LPKR MNKLGSGGAP GTGSFLFPDP AVEHEALTEA AHASEHKSLT ALKEHQDRIH G

UniProtKB: Cytochrome bc1 complex cytochrome b subunit

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Macromolecule #3: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 21.221863 KDa
SequenceString: CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFADG FATVTIETTT PGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ VRADGSGKLV TTTDAFTAED L LDGAKTAI ...String:
CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFADG FATVTIETTT PGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ VRADGSGKLV TTTDAFTAED L LDGAKTAI IIHEKADNFA NIPPERYQQV NGAPGPDQTT MATGDAGSRV ACGVISAG

UniProtKB: Superoxide dismutase [Cu-Zn]

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Macromolecule #4: Cytochrome aa3 subunit 2

MacromoleculeName: Cytochrome aa3 subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 35.201008 KDa
SequenceString: WSDALALGWP TGITPEAKLN RELWIGSVIA SFAVGAIVWG LIFWTSAFHR KKATDTELPR QFGYNMPLEL TLTVIPFLII SVLFYFTVV VQERMMHKDP NPEVVIDVTA FQWNWKFGYQ KIAFADGSFD YDGADPERKE AMTSRPEGKD EHGIEKVGPI R GMTPEDRT ...String:
WSDALALGWP TGITPEAKLN RELWIGSVIA SFAVGAIVWG LIFWTSAFHR KKATDTELPR QFGYNMPLEL TLTVIPFLII SVLFYFTVV VQERMMHKDP NPEVVIDVTA FQWNWKFGYQ KIAFADGSFD YDGADPERKE AMTSRPEGKD EHGIEKVGPI R GMTPEDRT YLNFDKIETL GTSSEIPVLV LPAGKRIEFV LNSADVIHGF WVPEFLFKRD VLPEPKANNS DNVFQVSEIQ QT GAFVGRC TEMCGTFHAM MNFEVRVVEP NDFKAYIDQR NAGKTNAEAL AAINQPPLAI TTEPFESRRG ELVPQ

UniProtKB: cytochrome-c oxidase

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Macromolecule #5: Cytochrome aa3 subunit 3

MacromoleculeName: Cytochrome aa3 subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 22.196883 KDa
SequenceString: MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS ...String:
MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS KFTPAQATAA IVVSYYWHFV DIVWIALFAT IYFVR

UniProtKB: Probable cytochrome c oxidase subunit 3

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Macromolecule #6: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.177424 KDa
SequenceString:
MHIEARLFEI LTAFFALAAV VYAVLTAMFA TGGVEWAGTT ALVLTTGLTL ITGTFFRFVA RRLDTRPEDY EDAEISDGAG ELGFFAPHS WWPILISLSF STAAVGAALW LPWLIAAGVA FVITSVCGLV FEYYWGPEKH

UniProtKB: Cytochrome c oxidase polypeptide 4

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Macromolecule #7: Cytochrome c oxidase subunit CtaJ

MacromoleculeName: Cytochrome c oxidase subunit CtaJ / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.365549 KDa
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

UniProtKB: Uncharacterized protein

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Macromolecule #8: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.808747 KDa
SequenceString:
ELDLPYGSAL TSSGRISAVT EPGELSVHYP FPTMDLVVLD DALKYGSRAA KARFAVYIGP LGADTAATAR EILANVPTPE NAVLLAVSP DQRAIEVVYG ADVKGRGIES AAPLGVSAAA ASFKEGNLID GLISAVRVMS AGVSPA

UniProtKB: Uncharacterized protein MSMEG_4692/MSMEI_4575

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Macromolecule #9: Conserved transmembrane protein

MacromoleculeName: Conserved transmembrane protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.329909 KDa
SequenceString:
MSSTQDRSQL DPEEQPVANT EVERHTGVDV EDVPSAEWGW SHMPIGVMHI GGLLSAAFLL VMMRGNHVGH VEDWFLIGFA AVIVALVGR NWWLRRRGWI R

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Macromolecule #10: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 23.18399 KDa
SequenceString: QSALLRTGKQ LFETSCVSCH GANLQGVPDR GPSLIGTGEA AVYFQVSTGR MPAMRGEAQA PSKPPHFDES QIDALGAYVQ ANGGGPTVP RDDHGAVAQE SLIGGDVARG GDLFRLNCAS CHNFTGKGGA LSSGKYAPDL GDANPAQIYT AMLTGPQNMP K FSDRQLTP ...String:
QSALLRTGKQ LFETSCVSCH GANLQGVPDR GPSLIGTGEA AVYFQVSTGR MPAMRGEAQA PSKPPHFDES QIDALGAYVQ ANGGGPTVP RDDHGAVAQE SLIGGDVARG GDLFRLNCAS CHNFTGKGGA LSSGKYAPDL GDANPAQIYT AMLTGPQNMP K FSDRQLTP DEKRDIVAYV RESAETPSYG GYGLGGFGPA PEGMAMWIIG MVAAIGVAMW IGSRA

UniProtKB: Cytochrome bc1 complex cytochrome c subunit

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Macromolecule #11: LpqE protein

MacromoleculeName: LpqE protein / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.412873 KDa
SequenceString:
CSAGQISQTT TQEPAVNGVN AQAGQVSLRN VHLRAPQQTD YVEPGTTVEL LFVAANDSTE GSNKLKSITS DVGEVTLTGD STVPADGVL IVGEPDGQIQ AVENAEAADA VTAEVELTKP ITNGLLYDFT FTFEDGETTV AVPISAGEQP RRPVPPAGPG

UniProtKB: LpqE protein

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Macromolecule #12: Cytochrome bc1 complex Rieske iron-sulfur subunit

MacromoleculeName: Cytochrome bc1 complex Rieske iron-sulfur subunit / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 42.210484 KDa
SequenceString: GQPTDAELAE MSREELVKLG GKIDGVETIF KEPRWPVPGT KAEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLA TPLYGLTFGL SILSIGIGAV LFQKKFIPEE ISVQDRHDGR SPEVHRKTVA ANLTDALEGS TLKRRKVIGL S LGIGLGAF ...String:
GQPTDAELAE MSREELVKLG GKIDGVETIF KEPRWPVPGT KAEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLA TPLYGLTFGL SILSIGIGAV LFQKKFIPEE ISVQDRHDGR SPEVHRKTVA ANLTDALEGS TLKRRKVIGL S LGIGLGAF GAGTLVAFIG GLIKNPWKPV VPTAEGKKAV LWTSGWTPRF KGETIYLARA TGRPGESPFV KMRPEDIDAG GM ETVFPWR ESDGDGTTVE SEHKLTEIAM GVRNPVMLIR IKPADMHRVI KRKGQESFNF GELFAYTKVC SHLGCPSSLY EQQ TYRILC PCHQSQFDAL EFAKPIFGPA ARALAQLPIT IDEDGYLVAN GDFVEPVGPA FWERKS

UniProtKB: Cytochrome bc1 complex Rieske iron-sulfur subunit

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Macromolecule #13: Probable malate:quinone oxidoreductase

MacromoleculeName: Probable malate:quinone oxidoreductase / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: malate dehydrogenase (quinone)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 54.970414 KDa
SequenceString: MSEANAGTNA KTDVVLVGAG IMSATLGTLI KLLEPNWSIT MIERLDGAAA ESSDPWNNAG TGHSALCELN YTPALPDGTI DISKAVNVN EQFQVSRQFW AHAVENGVLP DVRSFLNPVP HVSFVYGADN VQYLKARYNA LVTNPLFASM EFIDDKDEFT R RLPLMAEK ...String:
MSEANAGTNA KTDVVLVGAG IMSATLGTLI KLLEPNWSIT MIERLDGAAA ESSDPWNNAG TGHSALCELN YTPALPDGTI DISKAVNVN EQFQVSRQFW AHAVENGVLP DVRSFLNPVP HVSFVYGADN VQYLKARYNA LVTNPLFASM EFIDDKDEFT R RLPLMAEK RDFSEPVALN WSQHGTDVDF GSLSRQLIGF AAGNGMTTMF GHDVRDLSKN SDGSWTVKVR NRRTGNNFKI NA KFVFVGA GGGALPLLQK SGIPEAKGFG GFPVGGAFLR TNKQHLTSRH NAKVYGLPPL GAPPMSVPHL DTRVINGRQW LLF GPFAGW SPKFLKQGKV TDLPLSVKPN NLASMLGVGL TEVGLLKYLI GQLLLSEPAR VETLREFAPS AVDSDWELDI AGQR VQVIR RKGAGGVLEF GTTVLAAADG SIAGLLGASP GASTAVPAML DVLQRCFADR YQAWTPKLKE MVPSLGTKLS DEPKL FEEV WSWGTKVLKL DVQANTAEAA NAPATV

UniProtKB: Probable malate:quinone oxidoreductase

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Macromolecule #14: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 14 / Number of copies: 6 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #15: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 15 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 16 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #17: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 17 / 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 #18: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 18 / Number of copies: 8 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #19: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)...

MacromoleculeName: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
type: ligand / ID: 19 / Number of copies: 6 / Formula: 9Y0
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-9Y0:
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate

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Macromolecule #20: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 20 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #21: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 21 / Number of copies: 4 / Formula: 9XX
Molecular weightTheoretical: 594.992 Da
Chemical component information

ChemComp-9XX:
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

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Macromolecule #22: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 22 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #23: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...

MacromoleculeName: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
type: ligand / ID: 23 / Number of copies: 8 / Formula: 9YF
Molecular weightTheoretical: 853.112 Da
Chemical component information

ChemComp-9YF:
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate

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Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 24 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 41.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145585
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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