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- EMDB-0289: Structure of a functional obligate respiratory supercomplex from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0289
TitleStructure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Map dataRespiratory supercomplex from Mycobacterium smegmatisSupercomplex
Sample
  • Complex: Respiratory Supercomplex from Mycobacterium smegmatisSupercomplex
    • Protein or peptide: x 13 types
  • Ligand: x 7 types
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / respiratory electron transport chain ...aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / 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, subunit I bacterial type / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like ...Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / 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, 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 / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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 b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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. / 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
Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Cytochrome c oxidase subunit 1 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / Cytochrome bc1 complex cytochrome b subunit
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Mycobacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWiseman B / Nitharwal RG / Fedotovskaya O / Schafer J / Guo H / Kuang Q / Benlekbir S / Sjostrand D / Adelroth P / Rubinstein JL ...Wiseman B / Nitharwal RG / Fedotovskaya O / Schafer J / Guo H / Kuang Q / Benlekbir S / Sjostrand D / Adelroth P / Rubinstein JL / Brzezinski P / Hogbom M
Funding support Canada, Sweden, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchMOP 81294 Canada
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of a functional obligate complex IIIIV respiratory supercomplex from Mycobacterium smegmatis.
Authors: Benjamin Wiseman / Ram Gopal Nitharwal / Olga Fedotovskaya / Jacob Schäfer / Hui Guo / Qie Kuang / Samir Benlekbir / Dan Sjöstrand / Pia Ädelroth / John L Rubinstein / Peter Brzezinski / Martin Högbom /
Abstract: In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is ...In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is coupled to transmembrane proton translocation, thus establishing the electrochemical proton gradient that drives ATP synthesis. We isolated, biochemically characterized, and determined the structure of the obligate IIIIV supercomplex from Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The supercomplex has quinol:O oxidoreductase activity without exogenous cytochrome c and includes a superoxide dismutase subunit that may detoxify reactive oxygen species produced during respiration. We found menaquinone bound in both the Q and Q sites of complex III. The complex III-intrinsic diheme cytochrome cc subunit, which functionally replaces both cytochrome c and soluble cytochrome c in canonical electron-transport chains, displays two conformations: one in which it provides a direct electronic link to complex IV and another in which it serves as an electrical switch interrupting the connection.
History
DepositionOct 12, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseNov 7, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.475
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.475
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hwh
  • Surface level: 0.475
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0289.png

Downloads & links

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Map

FileDownload / File: emd_0289.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRespiratory supercomplex from Mycobacterium smegmatis
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.475 / Movie #1: 0.475
Minimum - Maximum-3.9200296 - 5.8836565
Average (Standard dev.)0.009659335 (±0.12999378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 402.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z402.800402.800402.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-3.9205.8840.010

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Supplemental data

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Sample components

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Entire : Respiratory Supercomplex from Mycobacterium smegmatis

EntireName: Respiratory Supercomplex from Mycobacterium smegmatisSupercomplex
Components
  • Complex: Respiratory Supercomplex from Mycobacterium smegmatisSupercomplex
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: Co-purified unknown transmembrane helices built as polyALA
    • Protein or peptide: Co-purified unknown transmembrane helices built as polyALA
    • Protein or peptide: Co-purified unknown peptide built as polyALA
    • Protein or peptide: Co-purified unknown peptide built as polyALA
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: MSMEG_4693
    • Protein or peptide: Uncharacterized protein MSMEG_4692/MSMEI_4575
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Ubiquinol-cytochrome C reductase QcrB
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CARDIOLIPIN
  • Ligand: MENAQUINONE-9Vitamin K2
  • Ligand: COPPER (II) ION
  • Ligand: HEME-AS
  • Ligand: HEME C
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Respiratory Supercomplex from Mycobacterium smegmatis

SupramoleculeName: Respiratory Supercomplex from Mycobacterium smegmatis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: deletion of the complex III operon qcrCAB (qcrCAB::hyg)
Location in cell: membrane
Molecular weightExperimental: 770 KDa

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Macromolecule #1: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 44.869395 KDa
SequenceString: MDRIASMSQD SPDIKGTDAP GQTGVPGQPT DAELAEMSRE ELVKLGGKID GVETIFKEPR WPVPGTKAEK RTERLVAYWL MLGGLSGLA LLLVFLFWPW EYQPFGSEGE FLYSLATPLY GLTFGLSILS IGIGAVLFQK KFIPEEISVQ DRHDGRSPEV H RKTVAANL ...String:
MDRIASMSQD SPDIKGTDAP GQTGVPGQPT DAELAEMSRE ELVKLGGKID GVETIFKEPR WPVPGTKAEK RTERLVAYWL MLGGLSGLA LLLVFLFWPW EYQPFGSEGE FLYSLATPLY GLTFGLSILS IGIGAVLFQK KFIPEEISVQ DRHDGRSPEV H RKTVAANL TDALEGSTLK RRKVIGLSLG IGLGAFGAGT LVAFIGGLIK NPWKPVVPTA EGKKAVLWTS GWTPRFKGET IY LARATGR PGESPFVKMR PEDIDAGGME TVFPWRESDG DGTTVESEHK LTEIAMGVRN PVMLIRIKPA DMHRVIKRKG QES FNFGEL FAYTKVCSHL GCPSSLYEQQ TYRILCPCHQ SQFDALEFAK PIFGPAARAL AQLPITIDED GYLVANGDFV EPVG PAFWE RKS

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Macromolecule #2: Co-purified unknown transmembrane helices built as polyALA

MacromoleculeName: Co-purified unknown transmembrane helices built as polyALA
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 6.315777 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Co-purified unknown transmembrane helices built as polyALA

MacromoleculeName: Co-purified unknown transmembrane helices built as polyALA
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 5.549833 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #4: Co-purified unknown peptide built as polyALA

MacromoleculeName: Co-purified unknown peptide built as polyALA / type: protein_or_peptide / ID: 4
Details: chains M,K: transmembrane helix built and refined to density. chains i, j: homology model of soluble domain built as polyALA only rigid-body docked to density.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 1.720111 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #5: Co-purified unknown peptide built as polyALA

MacromoleculeName: Co-purified unknown peptide built as polyALA / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 2.996685 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #6: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 6
Details: chains M,K: transmembrane helix built and refined into density chains i,j: homology model of the periplasmic soluble domain built as polyALA and rigid-body docked into low resolution density
Number of copies: 4 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 27.874547 KDa
SequenceString: MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSLI GTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG DVARGGDLFR L NCASCHNF ...String:
MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSLI GTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG DVARGGDLFR L NCASCHNF TGKGGALSSG KYAPDLGDAN PAQIYTAMLT GPQNMPKFSD RQLTPDEKRD IVAYVRESAE TPSYGGYGLG GF GPAPEGM AMWIIGMVAA IGVAMWIGSR A

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Macromolecule #7: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 38.077465 KDa
SequenceString: MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT ...String:
MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT SRPEGKDEHG IEKVGPIRGM TPEDRTYLNF DKIETLGTSS EIPVLVLPAG KRIEFVLNSA DVIHGFWVPE FL FKRDVLP EPKANNSDNV FQVSEIQQTG AFVGRCTEMC GTFHAMMNFE VRVVEPNDFK AYIDQRNAGK TNAEALAAIN QPP LAITTE PFESRRGELV PQASK

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Macromolecule #8: MSMEG_4693

MacromoleculeName: MSMEG_4693 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 8.365549 KDa
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

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Macromolecule #9: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 15.910971 KDa
SequenceString:
MASGDIATVA NAELDLPYGS ALTSSGRISA VTEPGELSVH YPFPTMDLVV LDDALKYGSR AAKARFAVYI GPLGADTAAT AREILANVP TPENAVLLAV SPDQRAIEVV YGADVKGRGI ESAAPLGVSA AAASFKEGNL IDGLISAVRV MSAGVSPA

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Macromolecule #10: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 64.841637 KDa
SequenceString: MTTHAPSAGE LLARRPFPQR LGPRWTLLYK LVTTTDHKLI GMMYVVACFI FFFIGGLMAL LLRTELAVPG LQFLSNEQYN QLFTMHGTV MLLFYATPIV FGFANLVVPL QIGAPDVAFP RLNALSFWLF LFGASIALGG FLAPGGPADF GWTAYTPLSN A MHSPGAGG ...String:
MTTHAPSAGE LLARRPFPQR LGPRWTLLYK LVTTTDHKLI GMMYVVACFI FFFIGGLMAL LLRTELAVPG LQFLSNEQYN QLFTMHGTV MLLFYATPIV FGFANLVVPL QIGAPDVAFP RLNALSFWLF LFGASIALGG FLAPGGPADF GWTAYTPLSN A MHSPGAGG DLWIFGLIVG GLGTILGAVN MITTVVCMRA PGMIMFRMPI FTWNILVTSV IVLVAFPLLT SALFGLAADR NL GAHVFDP ANGGTMLWEH LFWFFGHPEV YIIALPFFGI VTEIFPVFSR KPVFGYTTLV YATISIGALS IAVWAHHLYA TGA VLLPFF SFMTFMIAVP TGIKFVNWIG TMWKGQLTFE TPMLFSVGFL VTFLLGGLTG VILASPPLDF HVTDSYFVVA HFHY VLFGT IVFATYAGVY FWFPKMTGRL LDDRLGKLHF WLTLIGFHTT FLVHHWLGAE GMPRRYADYL PTDGFTTLNI VSTIG SFIL GVSMLPFVWN VFKSWRYGEP VTVDDPWGYG NSLEWATSCP PPRHNFTELP RIRSERPAFE LHYPHMIERL RAESHP GRT QGGPGAVTLP QPQARSHPVE

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Macromolecule #11: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
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 #12: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
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 #13: Ubiquinol-cytochrome C reductase QcrB

MacromoleculeName: Ubiquinol-cytochrome C reductase QcrB / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 61.271945 KDa
Recombinant expressionOrganism: Mycobacterium smegmatis MC2 155 (bacteria)
SequenceString: MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGFFGY S LPDDLLSG ...String:
MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGFFGY S LPDDLLSG TGIRAALSGI TMGIPVIGTW MHWALFGGDF PGEILIPRLY ALHILLIPGI ILALIGAHLA LVWFQKHTQF PG PGRTETN VVGVRVMPVF AVKSGAFFAM ITGVLGLMGG LLTINPIWNL GPYKPSQVSA GSQPDFYMMW TDGLIRLWPA WEF YPFGHT IPQGVWVAVG MGLVFALLIA YPFIEKKVTG DDAHHNLLQR PRDVPVRTAI GSMAIALYLL LTFACMNDII ALKF HISLN ATTWIGRIGM VVLPAIVYFV AYRWAISLQR SDREVLEHGV ETGIIKRLPH GAYVELHQPL GPVDEHGHPI PLEYA GAPL PKRMNKLGSG GAPGTGSFLF PDPAVEHEAL TEAAHASEHK SLTALKEHQD RIHGNGETNG HHDYKDDDDK

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Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 14 / 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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Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #16: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 16 / Number of copies: 4 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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Macromolecule #17: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 17 / 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 #18: HEME-AS

MacromoleculeName: HEME-AS / type: ligand / ID: 18 / Number of copies: 4 / Formula: HAS
Molecular weightTheoretical: 920.954 Da
Chemical component information

ChemComp-HAS:
HEME-AS

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Macromolecule #19: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 19 / 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 #20: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 20 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 40 seconds at 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5316 / Average exposure time: 60.0 sec. / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 751329
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 104198
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModel was built de novo; except for chains i,j which are polyALA homology models rigid-body docked into low resolution density.
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Cross-correlation coefficient
Output model

PDB-6hwh:
Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis

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