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- EMDB-9610: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis -

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Basic information

Entry
Database: EMDB / ID: EMD-9610
TitleRespiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
Map data
Sample
  • Complex: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV supercomplex from Mycobacterium smegmatis
    • Protein or peptide: x 12 types
  • Ligand: x 11 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 / superoxide dismutase / superoxide dismutase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...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 / superoxide dismutase / superoxide dismutase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / aerobic respiration / respiratory electron transport chain / monooxygenase activity / 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 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, 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 / 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 / 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. / 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
Cytochrome c oxidase subunit 1 / Superoxide dismutase [Cu-Zn] / Uncharacterized protein / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / LpqE protein ...Cytochrome c oxidase subunit 1 / Superoxide dismutase [Cu-Zn] / Uncharacterized protein / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / LpqE protein / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit
Similarity search - Component
Biological speciesMycobacterium smegmatis MC2 51 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXu A / Gong HR / Ji WX / Gao RG / Wang SH / Li J / Wang Q / Rao ZH
Funding support China, 6 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFC0840300 China
Ministry of Science and Technology (China)2014CB542800 China
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China813300237 China
Ministry of Science and Technology (China)2014CBA02003 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Science / Year: 2018
Title: An electron transfer path connects subunits of a mycobacterial respiratory supercomplex.
Authors: Hongri Gong / Jun Li / Ao Xu / Yanting Tang / Wenxin Ji / Ruogu Gao / Shuhui Wang / Lu Yu / Changlin Tian / Jingwen Li / Hsin-Yung Yen / Sin Man Lam / Guanghou Shui / Xiuna Yang / Yuna Sun / ...Authors: Hongri Gong / Jun Li / Ao Xu / Yanting Tang / Wenxin Ji / Ruogu Gao / Shuhui Wang / Lu Yu / Changlin Tian / Jingwen Li / Hsin-Yung Yen / Sin Man Lam / Guanghou Shui / Xiuna Yang / Yuna Sun / Xuemei Li / Minze Jia / Cheng Yang / Biao Jiang / Zhiyong Lou / Carol V Robinson / Luet-Lok Wong / Luke W Guddat / Fei Sun / Quan Wang / Zihe Rao /
Abstract: We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from It comprises a complex III dimer flanked on either side by individual complex IV ...We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis.
History
DepositionAug 1, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseNov 14, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6adq
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6adq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9610.png

Downloads & links

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Map

FileDownload / File: emd_9610.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.0452 / Movie #1: 0.0452
Minimum - Maximum-0.27065414 - 0.5625258
Average (Standard dev.)0.0002480549 (±0.016874203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 379.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z292292292
origin x/y/z0.0000.0000.000
length x/y/z379.600379.600379.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS292292292
D min/max/mean-0.2710.5630.000

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Supplemental data

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Mask #1

Fileemd_9610_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_9610_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_9610_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Superoxide dismutase in complex with bcc-aa3 type CIII-CIV superc...

EntireName: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV supercomplex from Mycobacterium smegmatis
Components
  • Complex: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV supercomplex from Mycobacterium smegmatis
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase 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: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
    • Protein or peptide: LpqE protein
    • Protein or peptide: Ubiquinol-cytochrome c reductase cytochrome b subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Rieske iron-sulfur protein QcrA
  • 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: PALMITIC ACID
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • 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: MENAQUINONE-9Vitamin K2
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV superc...

SupramoleculeName: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV supercomplex from Mycobacterium smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightExperimental: 800 KDa

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Macromolecule #1: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (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 #2: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 64.162965 KDa
SequenceString: MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG ...String:
MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG DLWIMGLAVG GLGTILGGVN MITTVVCMRA PGMTMFRMPI FTWNILVTSI LVLIAFPILT AALFGLAADR HL GAHIYDP ANGGVLLWQH LFWFFGHPEV YIIALPFFGI VSEIFPVFSR KPIFGYTTLI YATLAIAALS VAVWAHHMYA TGA VLLPFF SFMTFLIAVP TGIKFFNWIG TMWKGQLTFE TPMLFSVGFL ITFLLGGLSG VLLASPPLDF HVTDSYFVIA HFHY VLFGT IVFATYAGIY FWFPKMTGRL LDERLGKLHF WLTFIGFHTT FLVQHWLGDE GMPRRYADYL PTDGFTTLNV ISTVG AFIL GVSMLPFVWN VFKSWRYGEP VTVDDPWGYG NSLEWATSCP PPRHNFTELP RIRSERPAFE LHYPHMVERM RAEAHV GRA HHPELETADK SS

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Macromolecule #3: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (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 #4: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (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 #5: Cytochrome c oxidase subunit CtaJ

MacromoleculeName: Cytochrome c oxidase subunit CtaJ / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 8.365549 KDa
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

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Macromolecule #6: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (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 #7: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1

MacromoleculeName: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 11.329909 KDa
SequenceString:
MSSTQDRSQL DPEEQPVANT EVERHTGVDV EDVPSAEWGW SHMPIGVMHI GGLLSAAFLL VMMRGNHVGH VEDWFLIGFA AVIVALVGR NWWLRRRGWI R

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Macromolecule #8: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 23.232375 KDa
SequenceString: MLKPVSVAVL FATPVLALSA CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFAD GFATVTIETT TPGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ V RADGSGKL ...String:
MLKPVSVAVL FATPVLALSA CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFAD GFATVTIETT TPGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ V RADGSGKL VTTTDAFTAE DLLDGAKTAI IIHEKADNFA NIPPERYQQV NGAPGPDQTT MATGDAGSRV ACGVISAG

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Macromolecule #9: LpqE protein

MacromoleculeName: LpqE protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 19.118969 KDa
SequenceString:
MNRFSSRAGL AVCGLATAVA LTACSAGQIS QTTTQEPAVN GVNAQAGQVS LRNVHLRAPQ QTDYVEPGTT VELLFVAAND STEGSNKLK SITSDVGEVT LTGDSTVPAD GVLIVGEPDG QIQAVENAEA ADAVTAEVEL TKPITNGLLY DFTFTFEDGE T TVAVPISA GEQPRRPVPP AGPGSSEH

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Macromolecule #10: Ubiquinol-cytochrome c reductase cytochrome b subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase cytochrome b subunit / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 60.27498 KDa
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 HH

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Macromolecule #11: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 30.857109 KDa
SequenceString: MDRAVRHHLL RPMNIGSPMS SMRRGSMTSK SRRRLRRRLS AGLLLLIGLA VAGGVAATLT PQPQVAVADE SQSALLRTGK QLFETSCVS CHGANLQGVP DRGPSLIGTG EAAVYFQVST GRMPAMRGEA QAPSKPPHFD ESQIDALGAY VQANGGGPTV P RDDHGAVA ...String:
MDRAVRHHLL RPMNIGSPMS SMRRGSMTSK SRRRLRRRLS AGLLLLIGLA VAGGVAATLT PQPQVAVADE SQSALLRTGK QLFETSCVS CHGANLQGVP DRGPSLIGTG EAAVYFQVST GRMPAMRGEA QAPSKPPHFD ESQIDALGAY VQANGGGPTV P RDDHGAVA QESLIGGDVA RGGDLFRLNC ASCHNFTGKG GALSSGKYAP DLGDANPAQI YTAMLTGPQN MPKFSDRQLT PD EKRDIVA YVRESAETPS YGGYGLGGFG PAPEGMAMWI IGMVAAIGVA MWIGSRA

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Macromolecule #12: Rieske iron-sulfur protein QcrA

MacromoleculeName: Rieske iron-sulfur protein QcrA / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Molecular weightTheoretical: 46.383066 KDa
SequenceString: MDYRNGGRHR CGHVDRIASM SQDSPDIKGT DAPGQTGVPG QPTDAELAEM SREELVKLGG KIDGVETIFK EPRWPVPGTK AEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLAT PLYGLTFGLS ILSIGIGAVL FQKKFIPEEI S VQDRHDGR ...String:
MDYRNGGRHR CGHVDRIASM SQDSPDIKGT DAPGQTGVPG QPTDAELAEM SREELVKLGG KIDGVETIFK EPRWPVPGTK AEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLAT PLYGLTFGLS ILSIGIGAVL FQKKFIPEEI S VQDRHDGR SPEVHRKTVA ANLTDALEGS TLKRRKVIGL SLGIGLGAFG AGTLVAFIGG LIKNPWKPVV PTAEGKKAVL WT SGWTPRF KGETIYLARA TGRPGESPFV KMRPEDIDAG GMETVFPWRE SDGDGTTVES EHKLTEIAMG VRNPVMLIRI KPA DMHRVI KRKGQESFNF GELFAYTKVC SHLGCPSSLY EQQTYRILCP CHQSQFDALE FAKPIFGPAA RALAQLPITI DEDG YLVAN GDFVEPVGPA FWERKS

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Macromolecule #13: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 13 / Number of copies: 8 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #14: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 14 / 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 #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 18 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #16: (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: 16 / Number of copies: 8 / 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 #17: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 17 / 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 #18: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 18 / 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 #19: (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: 19 / 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 #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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Macromolecule #21: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 21 / Number of copies: 10 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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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 / Heme C

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Macromolecule #23: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 23 / 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

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 46.4 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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 202215
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6adq:
Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis

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