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- PDB-8ovc: Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 8ovc
TitleRespiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Components
  • (Co-purified unknown ...) x 2
  • (Cytochrome bc1 complex cytochrome c ...) x 2
  • (Cytochrome c oxidase ...) x 3
  • Cytochrome bc1 complex cytochrome b subunit
  • LpqE protein
  • Probable cytochrome c oxidase subunit 3
  • Superoxide dismutase [Cu-Zn]
  • Transmembrane protein
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
  • cytochrome-c oxidase
KeywordsELECTRON TRANSPORT / RESPIRATORY SUPERCOMPLEX / MEMBRANE PROTEIN / ACTINOBACTERIA
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / : / electron transport coupled proton transport ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / 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 DUF2631 / Protein of unknown function (DUF2631) / 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 ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / 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 / 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 c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein / 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-7PH / Chem-9XX / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 ...Chem-7PH / Chem-9XX / 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 c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / LpqE protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKovalova, T. / Krol, S. / Sjostrand, D. / Riepl, D. / Gamiz-Hernandez, A. / Brzezinski, P. / Kaila, V. / Hogbom, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2019.0043 Sweden
CitationJournal: Nat Commun / Year: 2024
Title: Long-range charge transfer mechanism of the IIIIV mycobacterial supercomplex.
Authors: Daniel Riepl / Ana P Gamiz-Hernandez / Terezia Kovalova / Sylwia M Król / Sophie L Mader / Dan Sjöstrand / Martin Högbom / Peter Brzezinski / Ville R I Kaila /
Abstract: Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing ...Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa IIIIV obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
History
DepositionApr 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Cytochrome bc1 complex cytochrome c subunit
M: Cytochrome bc1 complex cytochrome c subunit
N: Cytochrome bc1 complex cytochrome b subunit
P: Transmembrane protein
S: Probable cytochrome c oxidase subunit 3
T: Cytochrome c oxidase polypeptide 4
R: Cytochrome c oxidase subunit 1
Q: cytochrome-c oxidase
U: Cytochrome c oxidase subunit
V: Uncharacterized protein MSMEG_4692/MSMEI_4575
W: LpqE protein
Y: Superoxide dismutase [Cu-Zn]
E: Co-purified unknown peptide
F: Co-purified unknown peptide
C: Cytochrome bc1 complex cytochrome c subunit
G: Cytochrome bc1 complex cytochrome c subunit
H: Cytochrome bc1 complex cytochrome b subunit
I: Transmembrane protein
J: Probable cytochrome c oxidase subunit 3
K: Cytochrome c oxidase polypeptide 4
L: Cytochrome c oxidase subunit 1
X: cytochrome-c oxidase
Z: Cytochrome c oxidase subunit
a: Uncharacterized protein MSMEG_4692/MSMEI_4575
b: LpqE protein
c: Superoxide dismutase [Cu-Zn]
e: Co-purified unknown peptide
f: Co-purified unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)766,82797
Polymers712,16228
Non-polymers54,66669
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area231960 Å2
ΔGint-1928 kcal/mol
Surface area186230 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "O"
d_1ens_2chain "E"
d_2ens_2chain "f"
d_1ens_3chain "e"
d_2ens_3chain "F"
d_1ens_4(chain "H" and (resid 4 through 536 or (resid 604...
d_2ens_4(chain "N" and (resid 4 through 536 or (resid 605...
d_1ens_5(chain "I" and (resid 1 through 100 or resid 301))
d_2ens_5(chain "P" and (resid 1 through 100 or resid 301))
d_1ens_6(chain "J" and (resid 20 through 203 or (resid 301...
d_2ens_6(chain "S" and (resid 20 through 203 or (resid 301...
d_1ens_7chain "K"
d_2ens_7chain "T"
d_1ens_8(chain "L" and (resid 10 through 560 or resid 601 through 603))
d_2ens_8(chain "R" and (resid 10 through 560 or resid 601 through 603))
d_1ens_9(chain "b" and (resid 24 through 80 or resid 85...
d_2ens_9(chain "W" and (resid 24 through 80 or resid 86 through 87 or resid 89 through 182 or resid 202))
d_1ens_10(chain "Y" and (resid 21 through 45 or resid 301 through 302))
d_2ens_10chain "c"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNALAALACO72 - 29456 - 278
d_12ens_1HECHECHECHECCIB301
d_13ens_1HECHECHECHECCJB302
d_14ens_1MQ9MQ9MQ9MQ9HRB602
d_15ens_1MQ9MQ9MQ9MQ9CKB303
d_16ens_1WUOWUOWUOWUOCLB304
d_21ens_1GLNGLNALAALAOA72 - 29456 - 278
d_22ens_1HECHECHECHECOCA301
d_23ens_1HECHECHECHECODA302
d_24ens_1MQ9MQ9MQ9MQ9OEA303
d_25ens_1MQ9MQ9MQ9MQ9NIA601
d_26ens_1WUOWUOWUOWUOOFA304
d_11ens_2UNKUNKUNKUNKEM11 - 171 - 7
d_21ens_2UNKUNKUNKUNKfBA11 - 171 - 7
d_11ens_3UNKUNKUNKUNKeAA1 - 231 - 23
d_21ens_3UNKUNKUNKUNKFN1 - 231 - 23
d_11ens_4ASPASPILEILEHQ4 - 5364 - 536
d_12ens_4CDLCDLCDLCDLHTB604
d_13ens_4CDLCDLCDLCDLHUB605
d_14ens_4MQ9MQ9MQ9MQ9HWB607
d_15ens_4MQ9MQ9MQ9MQ9HYB609
d_16ens_4HEMHEMHEMHEMHZB610
d_21ens_4ASPASPILEILENC4 - 5364 - 536
d_22ens_4CDLCDLCDLCDLNKA603
d_23ens_4CDLCDLCDLCDLNLA604
d_24ens_4MQ9MQ9MQ9MQ9NMA605
d_25ens_4MQ9MQ9MQ9MQ9NNA606
d_26ens_4HEMHEMHEMHEMNOA607
d_11ens_5METMETARGARGIR1 - 1001 - 100
d_12ens_5CDLCDLCDLCDLICC301
d_21ens_5METMETARGARGPD1 - 1001 - 100
d_22ens_5CDLCDLCDLCDLPPA301
d_11ens_6ASNASNARGARGJS20 - 20320 - 203
d_12ens_6CDLCDLCDLCDLLGC601
d_13ens_67PH7PH7PH7PHJFC401
d_21ens_6ASNASNARGARGSE20 - 20320 - 203
d_22ens_6CDLCDLCDLCDLRTA601
d_23ens_67PH7PH7PH7PHSQA401
d_11ens_7METMETHISHISKT1 - 1391 - 139
d_12ens_7CDLCDLCDLCDLHAC611
d_21ens_7METMETHISHISTF1 - 1391 - 139
d_22ens_7CDLCDLCDLCDLTSA201
d_11ens_8GLUGLUVALVALLU10 - 56010 - 560
d_12ens_8HEAHEAHEAHEALHC602
d_13ens_8HEAHEAHEAHEALIC603
d_21ens_8GLUGLUVALVALRG10 - 56010 - 560
d_22ens_8HEAHEAHEAHEARUA602
d_23ens_8HEAHEAHEAHEARVA603
d_11ens_9CYSCYSASPASPbY24 - 8024 - 80
d_12ens_9SERSERASNASNbY85 - 8685 - 86
d_13ens_9LYSLYSILEILEbY89 - 12189 - 121
d_14ens_9ALAALAGLYGLYbY132 - 182132 - 182
d_15ens_99YF9YF9YF9YFbQC201
d_21ens_9CYSCYSASPASPWK24 - 8024 - 80
d_22ens_9ASNASNLYSLYSWK86 - 8786 - 87
d_23ens_9LYSLYSGLYGLYWK89 - 18289 - 182
d_24ens_99YF9YF9YF9YFWEB402
d_11ens_10CYSCYSPROPROYL21 - 4521 - 45
d_12ens_10PLMPLMPLMPLMYGB301
d_13ens_109XX9XX9XX9XXYHB302
d_21ens_10CYSCYSPROPROcZ21 - 4521 - 45
d_22ens_10PLMPLMPLMPLMcSC301
d_23ens_109XX9XX9XX9XXHBC612

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10

NCS oper:
IDCodeMatrixVector
1given(0.999755271614, -0.0179760289702, -0.0128941561199), (-0.0179629522388, -0.999838015433, 0.00112926634028), (-0.01291236719, -0.000897372866211, -0.999916229239)2.56362846732, 107.692036675, 227.229188726
2given(0.999846367983, -0.0175278084551, 0.000127912240635), (-0.0175017930579, -0.99871018171, -0.0476619364739), (0.000963156550204, 0.0476523753809, -0.998863515927)1.57267594388, 111.147080124, 221.801559356
3given(0.999930990661, -0.00716007333688, 0.00931382124144), (-0.00728130901573, -0.999888351659, 0.0130486303833), (0.00921935221826, -0.0131155467165, -0.999871484731)-1.54286408211, 104.761905529, 225.476744479
4given(0.999606712287, -0.0201409977573, -0.0195130971384), (-0.0198562618451, -0.999695102906, 0.0146775369525), (-0.0198027678906, -0.0142843072913, -0.999701860031)3.344009049, 106.024530122, 228.109336095
5given(0.999810415644, -0.0193294088826, -0.00234664068474), (-0.0193330020417, -0.999811947237, -0.00151828661405), (-0.00231685180971, 0.00156336637981, -0.999996094034)1.0557794146, 108.58543631, 226.027631668
6given(0.999851500867, -0.01350511298, -0.010704584903), (-0.0134680940663, -0.999903095435, 0.00352280889782), (-0.010751123512, -0.00337811540734, -0.999936498824)2.12367546789, 107.120535531, 227.402408255
7given(0.999866572749, -0.0135973100273, -0.00905261612022), (-0.0135364680477, -0.999885603565, 0.0067486159382), (-0.00914334355637, -0.00662517504007, -0.99993625113)1.76319206126, 106.551804104, 227.322550327
8given(0.999837919509, -0.0148361678317, -0.0101991586133), (-0.0148077844065, -0.999886288982, 0.00285282772117), (-0.0102403238875, -0.00270133839157, -0.999943917696)1.97498653522, 107.365502198, 227.288147397
9given(0.999875735479, -0.0104078591581, -0.0118401887261), (-0.010383361118, -0.999943825743, 0.0021286543934), (-0.0118616783474, -0.00200544892193, -0.999927636762)1.94272841323, 107.518507952, 227.243796898
10given(0.999972789495, -0.00709281176721, 0.00202787818715), (-0.00714158900468, -0.999658094216, 0.0251533770237), (0.00184877667532, -0.0251671748602, -0.999681546961)0.686222685112, 105.265871467, 227.215383371

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Components

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Cytochrome bc1 complex cytochrome c ... , 2 types, 4 molecules OCMG

#1: Protein Cytochrome bc1 complex cytochrome c subunit


Mass: 29109.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4261 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R050, quinol-cytochrome-c reductase
#2: Protein Cytochrome bc1 complex cytochrome c subunit


Mass: 44869.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4261 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R051, quinol-cytochrome-c reductase

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Protein , 7 types, 14 molecules NHPISJQXVaWbYc

#3: Protein Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 reductase complex subunit QcrB


Mass: 61514.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4263 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R052, quinol-cytochrome-c reductase
#4: Protein Transmembrane protein


Mass: 11329.909 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_2575 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QVH4
#5: Protein Probable cytochrome c oxidase subunit 3 / Cytochrome aa3 subunit 3


Mass: 22196.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4260 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R049
#8: Protein cytochrome-c oxidase / Cytochrome aa3 subunit 2


Mass: 38077.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4268 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R057, cytochrome-c oxidase
#10: Protein Uncharacterized protein MSMEG_4692/MSMEI_4575


Mass: 15910.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4692, MSMEI_4575 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R1B5
#11: Protein LpqE protein


Mass: 19118.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_6078 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R562
#12: Protein Superoxide dismutase [Cu-Zn]


Mass: 23232.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: sodC, MSMEG_0835 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QQQ1, superoxide dismutase

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Cytochrome c oxidase ... , 3 types, 6 molecules TKRLUZ

#6: 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 genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4267 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R056, cytochrome-c oxidase
#7: Protein Cytochrome c oxidase subunit 1


Mass: 64162.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: D806_022970 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A2U9PNL2, cytochrome-c oxidase
#9: Protein Cytochrome c oxidase subunit


Mass: 8365.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4693 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R1B6

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Co-purified unknown ... , 2 types, 4 molecules EfFe

#13: Protein/peptide Co-purified unknown peptide


Mass: 869.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Production host: Mycolicibacterium smegmatis (bacteria)
#14: Protein/peptide Co-purified unknown peptide


Mass: 2145.636 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Production host: Mycolicibacterium smegmatis (bacteria)

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Non-polymers , 15 types, 318 molecules

#15: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#16: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C56H80O2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-WUO / acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2) / [(2R)-2-[(10E,13E)-hexadeca-10,13-dienoyl]oxy-3-[[(1S,2R,3R,4S,5S,6R)-2-[(2R,3S,4S,5S,6R)-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2R,3S,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propyl] (10R)-10-methyloctadecanoate / phosphatidylinositol mannoside


Mass: 1415.802 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C72H135O24P
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#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.: 4 / Source method: obtained synthetically / Formula: C44H85O13P
#20: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#21: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#22: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H57O8P
#23: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#24: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#25: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#26: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#27: 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
#28: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: The respiratory supercomplex / Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 3.v / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90918 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.013747848
ELECTRON MICROSCOPYf_angle_d1.560564928
ELECTRON MICROSCOPYf_chiral_restr0.12536888
ELECTRON MICROSCOPYf_plane_restr0.01897976
ELECTRON MICROSCOPYf_dihedral_angle_d24.154517782
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2OCELECTRON MICROSCOPYNCS constraints1.41822130566
ens_2d_2MEELECTRON MICROSCOPYNCS constraints0.446782657412
ens_3d_2AAeELECTRON MICROSCOPYNCS constraints0.504643981619
ens_4d_2QHELECTRON MICROSCOPYNCS constraints5.20302378881
ens_5d_2RIELECTRON MICROSCOPYNCS constraints2.22776018084
ens_6d_2SJELECTRON MICROSCOPYNCS constraints1.71845287526
ens_7d_2TKELECTRON MICROSCOPYNCS constraints0.628423818359
ens_8d_2ULELECTRON MICROSCOPYNCS constraints0.733111793762
ens_9d_2YbELECTRON MICROSCOPYNCS constraints1.72067823934
ens_10d_2LYELECTRON MICROSCOPYNCS constraints1.56869471571

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