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

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Basic information

Entry
Database: PDB / ID: 8ovd
TitleRespiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Components
  • (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
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-7PH / Chem-9XX / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-7PH / Chem-9XX / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-IZL / MENAQUINONE-9 / PALMITIC ACID / TRIDECANE / : / 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: 2.3 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]
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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)768,729110
Polymers706,13224
Non-polymers62,59786
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area233260 Å2
ΔGint-1809 kcal/mol
Surface area166930 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "O"
d_2ens_1chain "C"
d_1ens_2chain "M"
d_2ens_2chain "G"
d_1ens_3chain "N"
d_2ens_3chain "H"
d_1ens_4(chain "P" and (resid 28 through 100 or resid 301))
d_2ens_4(chain "I" and (resid 28 through 100 or resid 301))
d_1ens_5(chain "S" and (resid 20 through 203 or (resid 301...
d_2ens_5(chain "J" and (resid 20 through 203 or (resid 301...
d_1ens_6chain "K"
d_2ens_6chain "T"
d_1ens_7(chain "R" and (resid 10 through 560 or resid 601 through 603 or resid 801))
d_2ens_7(chain "L" and (resid 10 through 560 or resid 601 through 603 or resid 901))
d_1ens_8chain "Q"
d_2ens_8(chain "X" and (resid 27 through 170 or resid 182 through 336 or resid 401 through 501))
d_1ens_9chain "V"
d_2ens_9chain "a"
d_1ens_10(chain "W" and (resid 24 through 182 or resid 202))
d_2ens_10(chain "b" and (resid 24 through 182 or resid 202))
d_1ens_11chain "c"
d_2ens_11chain "Y"

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_1GLNGLNALAALAOA72 - 29456 - 278
d_12ens_1HECHECHECHECOY301
d_13ens_1HECHECHECHECOZ302
d_14ens_1MQ9MQ9MQ9MQ9OAA303
d_15ens_1WUOWUOWUOWUOOBA304
d_21ens_1GLNGLNALAALACM72 - 29456 - 278
d_22ens_1HECHECHECHECCPB301
d_23ens_1HECHECHECHECCQB302
d_24ens_1MQ9MQ9MQ9MQ9CRB303
d_25ens_1WUOWUOWUOWUOCSB304
d_11ens_2GLNGLNLYSLYSMB41 - 42028 - 407
d_12ens_2FESFESFESFESMCA501
d_13ens_2IZLIZLIZLIZLMDA502
d_14ens_29YF9YF9YF9YFMEA503
d_15ens_27PH7PH7PH7PHHZB901
d_16ens_27PH7PH7PH7PHMFA504
d_21ens_2GLNGLNLYSLYSGN41 - 42028 - 407
d_22ens_2FESFESFESFESGVB902
d_23ens_2IZLIZLIZLIZLGWB903
d_24ens_29YF9YF9YF9YFGXB904
d_25ens_27PH7PH7PH7PHNPA609
d_26ens_27PH7PH7PH7PHGYB905
d_11ens_3ASPASPILEILENC4 - 5364 - 536
d_12ens_3HEMHEMHEMHEMNHA601
d_13ens_3CDLCDLCDLCDLNIA602
d_14ens_3CDLCDLCDLCDLNJA603
d_15ens_3CDLCDLCDLCDLNKA604
d_16ens_3MQ9MQ9MQ9MQ9NLA605
d_17ens_3MQ9MQ9MQ9MQ9GUB901
d_18ens_3MQ9MQ9MQ9MQ9NMA606
d_19ens_3HEMHEMHEMHEMNNA607
d_110ens_3MQ9MQ9MQ9MQ9NOA608
d_111ens_3MQ9MQ9MQ9MQ9TVA1301
d_21ens_3ASPASPILEILEHO4 - 5364 - 536
d_22ens_3HEMHEMHEMHEMHAC902
d_23ens_3CDLCDLCDLCDLHBC903
d_24ens_3CDLCDLCDLCDLHCC904
d_25ens_3CDLCDLCDLCDLHDC905
d_26ens_3MQ9MQ9MQ9MQ9HEC906
d_27ens_3MQ9MQ9MQ9MQ9MGA505
d_28ens_3MQ9MQ9MQ9MQ9HFC907
d_29ens_3HEMHEMHEMHEMHGC908
d_210ens_3MQ9MQ9MQ9MQ9HHC909
d_211ens_3MQ9MQ9MQ9MQ9KOC1301
d_11ens_4VALVALARGARGPD28 - 10028 - 100
d_12ens_4CDLCDLCDLCDLPQA301
d_21ens_4VALVALARGARGIP28 - 10028 - 100
d_22ens_4CDLCDLCDLCDLIIC301
d_11ens_5ASNASNARGARGSE20 - 20320 - 203
d_12ens_5CDLCDLCDLCDLRYA601
d_13ens_5TRDTRDTRDTRDSTA502
d_14ens_53PE3PE3PE3PESUA503
d_21ens_5ASNASNARGARGJQ20 - 20320 - 203
d_22ens_5CDLCDLCDLCDLLQC601
d_23ens_5TRDTRDTRDTRDJMC502
d_24ens_53PE3PE3PE3PEJNC503
d_11ens_6METMETHISHISKR1 - 1391 - 139
d_12ens_6CDLCDLCDLCDLCTB305
d_13ens_6TRDTRDTRDTRDKPC1302
d_21ens_6METMETHISHISTF1 - 1391 - 139
d_22ens_6CDLCDLCDLCDLTWA1302
d_23ens_6TRDTRDTRDTRDTXA1303
d_11ens_7GLUGLUVALVALRG10 - 56010 - 560
d_12ens_7HEAHEAHEAHEARZA602
d_13ens_7HEAHEAHEAHEARAB603
d_14ens_7CUCUCUCURBB604
d_15ens_7TRDTRDTRDTRDRFB608
d_21ens_7GLUGLUVALVALLS10 - 56010 - 560
d_22ens_7HEAHEAHEAHEALRC602
d_23ens_7HEAHEAHEAHEALSC603
d_24ens_7CUCUCUCULTC604
d_25ens_7TRDTRDTRDTRDLXC608
d_11ens_8TRPTRPVALVALQH27 - 33627 - 336
d_12ens_8CUCUCUCUQHB401
d_13ens_8CUCUCUCUQIB402
d_14ens_8TRDTRDTRDTRDQJB403
d_21ens_8TRPTRPARGARGXT27 - 17027 - 170
d_22ens_8VALVALVALVALXT182 - 336182 - 336
d_23ens_8CUCUCUCUXYC401
d_24ens_8CUCUCUCUXZC402
d_25ens_8TRDTRDTRDTRDXAD403
d_11ens_9ASPASPALAALAVJ15 - 15715 - 157
d_21ens_9ASPASPALAALAaV15 - 15715 - 157
d_11ens_10CYSCYSGLYGLYWK24 - 18224 - 182
d_12ens_109YF9YF9YF9YFWKB201
d_21ens_10CYSCYSGLYGLYbW24 - 18224 - 182
d_22ens_109YF9YF9YF9YFbBD201
d_11ens_11CYSCYSPROPROcX21 - 4521 - 45
d_12ens_11PLMPLMPLMPLMcED301
d_13ens_119XX9XX9XX9XXcFD302
d_21ens_11CYSCYSPROPROYL21 - 4521 - 45
d_22ens_11PLMPLMPLMPLMYNB301
d_23ens_119XX9XX9XX9XXYOB302

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10
ens_11

NCS oper:
IDCodeMatrixVector
1given(-0.999986231809, 0.00319488075763, 0.00416280298975), (-0.00318890228197, -0.999993875732, 0.00144201269744), (0.00416738455425, 0.00142871807159, 0.999990295788)178.322569968, 182.477460484, -0.637392268938
2given(-0.999999986574, 0.000163589635728, -9.55700311885E-6), (-0.000163590752534, -0.999999979778, 0.00011697361858), (-9.53786725393E-6, 0.000116975180447, 0.999999993113)178.833078062, 182.186256556, -0.00485678537505
3given(-0.999999979386, 0.000180462216795, -9.30617391014E-5), (-0.000180468648263, -0.999999981328, 6.91059226047E-5), (-9.30492663557E-5, 6.91227159064E-5, 0.999999993282)178.83784111, 182.169263032, 0.00306854690601
4given(-0.999974948083, -0.00702236705474, 0.00088857634545), (0.00702405435315, -0.999973506502, 0.00191022352992), (0.000875138513171, 0.00191641708371, 0.999997780737)179.513949606, 181.05533323, -0.459109063561
5given(-0.999999523476, 0.000856180206668, 0.000469044571594), (-0.000856190860257, -0.999999633215, -2.25130574064E-5), (0.000469025124322, -2.29146383536E-5, 0.999999889745)178.681087282, 182.245783326, -0.0344644446639
6given(-0.999997702787, 0.00179010353146, -0.00117896136855), (-0.0017902033349, -0.99999839409, 8.36038530724E-5), (-0.0011788098157, 8.57142415903E-5, 0.99999930153)178.904872305, 182.272480291, 0.0743958791909
7given(-0.999998915706, 0.00126392075137, -0.000755705778387), (-0.00126445105533, -0.999998954412, 0.000701667865146), (-0.000754818135655, 0.000702622657301, 0.999999468285)178.740928287, 182.261914109, -0.00447205189033
8given(-0.999998773143, 0.00151506452774, -0.000397859580704), (-0.00151511581032, -0.999998843939, 0.000128626442014), (-0.000397664243394, 0.000129229087549, 0.999999912581)178.626312852, 182.372456701, 0.0504552929686
9given(-0.99999481959, 0.00300425112323, 0.00115553778593), (-0.00300736956304, -0.999991815292, -0.00270648814851), (0.00114739735813, -0.00270994925696, 0.999995669818)178.365872197, 182.920309518, 0.125107115577
10given(-0.999993641125, -0.00319214918333, 0.00158993512429), (0.00318955590819, -0.999993583378, -0.0016309308976), (0.00159513109702, -0.00162584933974, 0.999997406082)179.135160237, 181.815445771, -0.0045724318465
11given(-0.999279105253, -0.03788774585, 0.0024059341647), (0.03790523112, -0.999251721402, 0.00769355107796), (0.00211264254773, 0.00777920232798, 0.999967509848)182.130076966, 179.933604577, -0.79068289576

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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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Non-polymers , 18 types, 700 molecules

#13: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#14: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C56H80O2
#15: 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
#16: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe2S2
#17: Chemical ChemComp-IZL / [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate


Mass: 1677.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C74H133O39P
#18: 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
#19: Chemical
ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C29H57O8P
#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.: 15 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#22: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C13H28
#23: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#24: Chemical
ChemComp-HEA / HEME-A


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 256.424 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H32O2
#30: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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, #3-#4, #6, #8-#12, #5, #7 / 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 IV / 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208243 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 17.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.014647962
ELECTRON MICROSCOPYf_angle_d1.44465007
ELECTRON MICROSCOPYf_chiral_restr0.12156875
ELECTRON MICROSCOPYf_plane_restr0.01937928
ELECTRON MICROSCOPYf_dihedral_angle_d24.767717965
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AOELECTRON MICROSCOPYNCS constraints1.363090069
ens_2d_2BMELECTRON MICROSCOPYNCS constraints0.770516832165
ens_3d_2CNELECTRON MICROSCOPYNCS constraints0.525250888951
ens_4d_2DPELECTRON MICROSCOPYNCS constraints1.43668857505
ens_5d_2ESELECTRON MICROSCOPYNCS constraints1.40155679965
ens_6d_2RKELECTRON MICROSCOPYNCS constraints0.627480654673
ens_7d_2GRELECTRON MICROSCOPYNCS constraints0.638381642146
ens_8d_2HQELECTRON MICROSCOPYNCS constraints0.636108051155
ens_9d_2JVELECTRON MICROSCOPYNCS constraints0.846518837187
ens_10d_2KWELECTRON MICROSCOPYNCS constraints0.751366521022
ens_11d_2XcELECTRON MICROSCOPYNCS constraints1.25779356873

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