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- PDB-6adq: Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6adq
TitleRespiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
Components
  • (Cytochrome c oxidase subunit ...) x 4
  • Cytochrome bc1 complex cytochrome c subunit
  • Cytochrome c oxidase polypeptide 4
  • LpqE protein
  • Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
  • Rieske iron-sulfur protein QcrA
  • Superoxide dismutase [Cu-Zn]
  • Ubiquinol-cytochrome c reductase cytochrome b subunit
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
KeywordsELECTRON TRANSPORT / Respiratory / Supercomplex / SOD / Mycobacterium / ETC / Lipoprotein
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
Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 ...Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / PALMITIC ACID / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGong, H.R. / Xu, A. / Gao, R.G. / Ji, W.X. / Wang, S.H. / Wang, Q. / Li, J. / Rao, Z.H.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFC0840300 China
Chinese Academy of SciencesXDB08020200 China
Ministry of Science and Technology (China)2014CB542800 China
Ministry of Science and Technology (China)2014CBA02003 China
National Natural Science Foundation of China813300237 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, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Assembly

Deposited unit
E: Cytochrome c oxidase subunit 2
F: Cytochrome c oxidase subunit 1
G: Cytochrome c oxidase subunit 3
H: Cytochrome c oxidase polypeptide 4
I: Cytochrome c oxidase subunit CtaJ
J: Uncharacterized protein MSMEG_4692/MSMEI_4575
D: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
Y: Superoxide dismutase [Cu-Zn]
K: LpqE protein
B: Ubiquinol-cytochrome c reductase cytochrome b subunit
C: Cytochrome bc1 complex cytochrome c subunit
A: Rieske iron-sulfur protein QcrA
Q: Cytochrome c oxidase subunit 2
R: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase subunit 3
T: Cytochrome c oxidase polypeptide 4
U: Cytochrome c oxidase subunit CtaJ
V: Uncharacterized protein MSMEG_4692/MSMEI_4575
P: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
Z: Superoxide dismutase [Cu-Zn]
W: LpqE protein
N: Ubiquinol-cytochrome c reductase cytochrome b subunit
O: Cytochrome bc1 complex cytochrome c subunit
M: Rieske iron-sulfur protein QcrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)769,56698
Polymers710,17524
Non-polymers59,39174
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome c oxidase subunit ... , 4 types, 8 molecules EQFRGSIU

#1: Protein Cytochrome c oxidase subunit 2 / / Cytochrome C oxidase subunit II ctaC


Mass: 38077.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R057, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase subunit 1 CtaD


Mass: 64162.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0A0D6HTJ9*PLUS, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase subunit 3 CtaE


Mass: 22196.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R049, cytochrome-c oxidase
#5: Protein Cytochrome c oxidase subunit CtaJ /


Mass: 8365.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R1B6

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Protein , 8 types, 16 molecules HTJVDPYZKWBNCOAM

#4: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15177.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R056, cytochrome-c oxidase
#6: Protein Uncharacterized protein MSMEG_4692/MSMEI_4575 / Cytochrome c oxidase subunit CtaI


Mass: 15910.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R1B5
#7: Protein Prokaryotic respiratory supercomplex associate factor 1 PRSAF1


Mass: 11329.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0QVH4*PLUS
#8: Protein Superoxide dismutase [Cu-Zn]


Mass: 23232.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0QQQ1, superoxide dismutase
#9: Protein LpqE protein


Mass: 19118.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R562
#10: Protein Ubiquinol-cytochrome c reductase cytochrome b subunit / Ubiquinol-cytochrome C reductase QcrB


Mass: 60274.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: A0R052
#11: Protein Cytochrome bc1 complex cytochrome c subunit / Ubiquinol-cytochrome C reductase QcrC


Mass: 30857.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: I7FPH1, quinol-cytochrome-c reductase
#12: Protein Rieske iron-sulfur protein QcrA


Mass: 46383.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium smegmatis MC2 51 (bacteria) / References: UniProt: I7GD61

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Non-polymers , 11 types, 74 molecules

#13: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#14: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical
ChemComp-9Y0 / (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C39H76NO8P
#17: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#18: Chemical
ChemComp-9XX / (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate / (S)-1-(palmitoyloxy)propan-2-yl (S)-10-methyloctadecanoate


Mass: 594.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H74O4
#19: Chemical
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


Mass: 853.112 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85O13P
#20: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#21: Chemical
ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C56H80O2
#22: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#23: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Sequence detailsSequence reference of entity 2/7 are available at NCBI with accession code WP_029104145.1 and WP_ ...Sequence reference of entity 2/7 are available at NCBI with accession code WP_029104145.1 and WP_003893930.1 respectively.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV supercomplex from Mycobacterium smegmatis
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 0.8 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium smegmatis MC2 51 (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 46.4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202215 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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