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- PDB-7qho: Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV... -

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Basic information

Entry
Database: PDB / ID: 7qho
TitleCytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (as isolated)
Components
  • (Cytochrome bc1 complex cytochrome ...) x 2
  • (Cytochrome c oxidase subunit ...) x 3
  • (Hypothetical membrane ...) x 2
  • (Uncharacterized ...) x 2
  • Actinobacterial supercomplex, subunit C (AscC)
  • Cytochrome bc1 complex Rieske iron-sulfur subunit
  • Cytochrome c oxidase polypeptide 4
  • Thiamine biosynthesis protein X
KeywordsOXIDOREDUCTASE / supercomplex / respiratory chain / cytochrome bcc-aa3 supercomplex / proton translocation / bioenergetics / membrane protein / electron transport
Function / homology
Function and homology information


thiamine biosynthetic process / 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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome ...thiamine biosynthetic process / 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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / respirasome / 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) / Neocarzinostatin-like / 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 ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Neocarzinostatin-like / 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 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, cbb3-type, subunit III / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / Cytochrome C oxidase subunit II, transmembrane domain superfamily / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / DIACYL GLYCEROL / FE2/S2 (INORGANIC) CLUSTER / HEME-AS / HEME C ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / DIACYL GLYCEROL / FE2/S2 (INORGANIC) CLUSTER / HEME-AS / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-IX7 / Chem-IZL / LYCOPENE / : / MENAQUINONE-9 / PALMITIC ACID / Thiamine biosynthesis protein X / Cytochrome c oxidase subunit 1 / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Uncharacterized protein Cgl2664/cg2949 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide 4 / Cytochrome bc1 complex cytochrome c subunit / Uncharacterized membrane protein Cgl2017/cg2211 / Uncharacterized protein / Hypothetical membrane protein / Hypothetical membrane protein / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKao, W.-C. / Hunte, C.
Funding support Germany, France, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)BIOSS EXC-294 Germany
German Research Foundation (DFG)CIBSS EXC-2189 Project ID 390939984 Germany
German Research Foundation (DFG)Project-ID 403222702 / SFB 1381 Germany
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-01 France
German Research Foundation (DFG)SCHI 871/11-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for safe and efficient energy conversion in a respiratory supercomplex.
Authors: Wei-Chun Kao / Claire Ortmann de Percin Northumberland / Tat Cheung Cheng / Julio Ortiz / Alexandre Durand / Ottilie von Loeffelholz / Oliver Schilling / Martin L Biniossek / Bruno P Klaholz / Carola Hunte /
Abstract: Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species ...Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa (III-IV) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Q site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis.
History
DepositionDec 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome bc1 complex Rieske iron-sulfur subunit
B: Cytochrome bc1 complex cytochrome b subunit
C: Cytochrome bc1 complex cytochrome c subunit
D: Cytochrome c oxidase subunit 1
E: Cytochrome c oxidase subunit 2
F: Cytochrome c oxidase subunit 3
G: Cytochrome c oxidase polypeptide 4
H: Uncharacterized protein Cgl2664/cg2949
I: Uncharacterized membrane protein Cgl2017/cg2211
J: Hypothetical membrane protein
K: Actinobacterial supercomplex, subunit C (AscC)
L: Hypothetical membrane protein
M: Thiamine biosynthesis protein X
N: Cytochrome bc1 complex Rieske iron-sulfur subunit
O: Cytochrome bc1 complex cytochrome b subunit
P: Cytochrome bc1 complex cytochrome c subunit
Q: Cytochrome c oxidase subunit 1
R: Cytochrome c oxidase subunit 2
S: Cytochrome c oxidase subunit 3
T: Cytochrome c oxidase polypeptide 4
U: Uncharacterized protein Cgl2664/cg2949
V: Uncharacterized membrane protein Cgl2017/cg2211
W: Hypothetical membrane protein
X: Actinobacterial supercomplex, subunit C (AscC)
Y: Hypothetical membrane protein
Z: Thiamine biosynthesis protein X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)767,912104
Polymers707,59826
Non-polymers60,31478
Water18010
1


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

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Components

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Protein , 4 types, 8 molecules ANGTKXMZ

#1: Protein Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 reductase complex subunit QcrA / Menaquinol--cytochrome c reductase iron-sulfur ...Cytochrome bc1 reductase complex subunit QcrA / Menaquinol--cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein


Mass: 45232.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: qcrA, Cgl2190, cg2404
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q79VE8
#7: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15557.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: ctaF, Cgl2194, cg2408
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NNK3, cytochrome-c oxidase
#11: Protein Actinobacterial supercomplex, subunit C (AscC)


Mass: 8373.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0818
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NS61
#13: Protein Thiamine biosynthesis protein X


Mass: 17152.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: thiX, Cgl2332, cg2561
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: P42461

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Cytochrome bc1 complex cytochrome ... , 2 types, 4 molecules BOCP

#2: Protein Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 reductase complex subunit QcrB / Menaquinol--cytochrome c reductase cytochrome b subunit


Mass: 59863.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: qcrB, Cgl2189, cg2403
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q79VE9, quinol-cytochrome-c reductase
#3: Protein Cytochrome bc1 complex cytochrome c subunit / Cytochrome c1 / Cytochrome bc1 reductase complex subunit Qcrc / Menaquinol--cytochrome c reductase ...Cytochrome c1 / Cytochrome bc1 reductase complex subunit Qcrc / Menaquinol--cytochrome c reductase cytochrome c subunit


Mass: 29898.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: qcrC, Cgl2191, cg2405
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NNK5, quinol-cytochrome-c reductase

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Cytochrome c oxidase subunit ... , 3 types, 6 molecules DQERFS

#4: Protein Cytochrome c oxidase subunit 1 / / Cytochrome aa3 subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 66340.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: ctaD, Cgl2523, cg2780
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q79VD7, cytochrome-c oxidase
#5: Protein Cytochrome c oxidase subunit 2 / / Cytochrome aa3 subunit 2 / Cytochrome c oxidase polypeptide II / Oxidase aa(3) subunit 2


Mass: 36811.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: ctaC, Cgl2195, cg2409
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NNK2, cytochrome-c oxidase
#6: Protein Cytochrome c oxidase subunit 3 / / Cytochrome aa3 subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 22457.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: ctaE, Cgl2192, cg2406
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q9AEL8, cytochrome-c oxidase

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Uncharacterized ... , 2 types, 4 molecules HUIV

#8: Protein Uncharacterized protein Cgl2664/cg2949 / P29


Mass: 16954.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl2664, cg2949
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NMB4
#9: Protein Uncharacterized membrane protein Cgl2017/cg2211 / P20


Mass: 16385.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl2017, cg2211
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NP09

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Hypothetical membrane ... , 2 types, 4 molecules JWLY

#10: Protein Hypothetical membrane protein


Mass: 12144.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0373
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NTD4
#12: Protein Hypothetical membrane protein


Mass: 6628.905 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0673
Production host: Corynebacterium glutamicum ATCC 13032 (bacteria)
References: UniProt: Q8NSJ8

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Sugars , 1 types, 2 molecules

#22: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 19 types, 86 molecules

#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#15: 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 / Feature type: SUBJECT OF INVESTIGATION
#16: 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 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C56H80O2 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#20: 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.: 14 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#21: Chemical ChemComp-LYC / LYCOPENE / Lycopene


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H77O8P / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C54H64FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / 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 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-IX7 / [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate


Mass: 1387.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C70H131O24P / Feature type: SUBJECT OF INVESTIGATION
#33: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: cytochrome bcc-aa3 supercomplex / Type: COMPLEX / Details: Cofactor-containing respiratory supercomplex / Entity ID: #1-#13 / Source: RECOMBINANT
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Source (recombinant)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding 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: 95 % / Chamber temperature: 283 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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1300 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.95 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3453

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cisTEM1.0.0CTF correction
7PHENIX1.19.2model fitting
9PHENIX1.19.2model refinement
10cisTEM1.0.0initial Euler assignment
11cisTEM1.0.0final Euler assignment
13cisTEM1.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 73863
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51060
Details: Reported by cisTEM, part-FSC using the 0.143 cut-off.
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 49.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006149820
ELECTRON MICROSCOPYf_angle_d0.905967774
ELECTRON MICROSCOPYf_chiral_restr0.04877300
ELECTRON MICROSCOPYf_plane_restr0.00588540
ELECTRON MICROSCOPYf_dihedral_angle_d13.710618344

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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