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- EMDB-24457: Mycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound -

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Basic information

Entry
Database: EMDB / ID: EMD-24457
TitleMycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound
Map dataMycobacterium CIII2CIV2 supercomplex, telacebec bound.
Sample
  • Complex: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
    • Protein or peptide: x 12 types
  • Ligand: x 12 types
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / respiratory electron transport chain ...aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / respiratory electron transport chain / monooxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / QcrA subunit, N-terminal / QcrA subunit N-terminal region / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / Cytochrome c oxidase subunit IV / Cytochrome b(N-terminal)/b6/petB ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / QcrA subunit, N-terminal / QcrA subunit N-terminal region / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / Cytochrome c oxidase subunit IV / Cytochrome b(N-terminal)/b6/petB / 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 / Cytochrome c/quinol oxidase subunit II / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Rieske iron-sulphur protein / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uncharacterized protein / 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: 3.0 Å
AuthorsDi Trani JM / Yanofsky DJ / Rubinstein JL
Funding support Canada, Sweden, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)JT162186 Canada
Knut and Alice Wallenberg Foundation2019.0043 Sweden
Swedish Research Council2018-04619 Sweden
CitationJournal: Elife / Year: 2021
Title: Structure of mycobacterial CIIICIV respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203).
Authors: David J Yanofsky / Justin M Di Trani / Sylwia Król / Rana Abdelaziz / Stephanie A Bueler / Peter Imming / Peter Brzezinski / John L Rubinstein /
Abstract: The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the ...The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIIICIV). In mycobacterial electron transport chains, CIIICIV replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified CIIICIV at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIIICIV both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIIICIV activity.
History
DepositionJul 16, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.82
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.82
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7rh7
  • Surface level: 0.82
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24457.png

Downloads & links

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Map

FileDownload / File: emd_24457.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium CIII2CIV2 supercomplex, telacebec bound.
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.82 / Movie #1: 0.82
Minimum - Maximum-4.052326 - 6.406744
Average (Standard dev.)-0.0023105105 (±0.18282953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 339.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z339.900339.900339.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-4.0526.407-0.002

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Supplemental data

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Sample components

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Entire : Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

EntireName: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
Components
  • Complex: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
    • Protein or peptide: LpqE protein
    • Protein or peptide: Cytochrome aa3 subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • 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: Superoxide dismutase [Cu-Zn]
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • Ligand: PALMITIC ACID
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: CARDIOLIPIN
  • Ligand: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
  • Ligand: MENAQUINONE-9Vitamin K2
  • 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

SupramoleculeName: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155

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Macromolecule #1: LpqE protein

MacromoleculeName: LpqE protein / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: Cytochrome aa3 subunit 2

MacromoleculeName: Cytochrome aa3 subunit 2 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 3 / 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: 61.733234 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 MRAEAHVG

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Macromolecule #4: Cytochrome aa3 subunit 3

MacromoleculeName: Cytochrome aa3 subunit 3 / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: Cytochrome c oxidase subunit CtaJ

MacromoleculeName: Cytochrome c oxidase subunit CtaJ / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / 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: 14.808747 KDa
SequenceString:
ELDLPYGSAL TSSGRISAVT EPGELSVHYP FPTMDLVVLD DALKYGSRAA KARFAVYIGP LGADTAATAR EILANVPTPE NAVLLAVSP DQRAIEVVYG ADVKGRGIES AAPLGVSAAA ASFKEGNLID GLISAVRVMS AGVSPA

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Macromolecule #8: Conserved transmembrane protein

MacromoleculeName: Conserved transmembrane protein / 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: 11.329909 KDa
SequenceString:
MSSTQDRSQL DPEEQPVANT EVERHTGVDV EDVPSAEWGW SHMPIGVMHI GGLLSAAFLL VMMRGNHVGH VEDWFLIGFA AVIVALVGR NWWLRRRGWI R

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Macromolecule #9: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
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

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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

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Macromolecule #11: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 11 / 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

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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

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Macromolecule #13: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 13 / 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 #14: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 14 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #15: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 15 / Number of copies: 6 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #16: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 16 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

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Macromolecule #17: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 17 / Number of copies: 16 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #18: (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: 18 / Number of copies: 4 / 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 #19: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 19 / Number of copies: 6 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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Macromolecule #20: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 20 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #21: (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: 21 / 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 #22: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 22 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #23: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperi...

MacromoleculeName: 6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
type: ligand / ID: 23 / Number of copies: 2 / Formula: HUU
Molecular weightTheoretical: 557.006 Da
Chemical component information

ChemComp-HUU:
6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide

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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 / Iron–sulfur 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-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 43.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70818

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7rh7:
Mycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound

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