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- PDB-5gup: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -

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Entry
Database: PDB / ID: 5gup
TitleCryo-EM structure of mammalian respiratory supercomplex I1III2IV1
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / Cryo-EM / Mammalian / Respiratory / Supercomplex
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein import / subthalamus development / pons development / respiratory chain complex III / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels ...TP53 Regulates Metabolic Genes / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein import / subthalamus development / pons development / respiratory chain complex III / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / oxidoreductase activity, acting on NAD(P)H / cerebellar Purkinje cell layer development / pyramidal neuron development / gliogenesis / mitochondrial respiratory chain complex III assembly / neural precursor cell proliferation / mitochondrial respiratory chain complex III / thalamus development / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex IV / oxygen sensor activity / anterograde axonal transport / ubiquinol-cytochrome-c reductase activity / mitochondrial respiratory chain complex I / electron transport coupled proton transport / acyl binding / cellular response to interferon-beta / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / ATP synthesis coupled electron transport / ubiquinone binding / mitochondrial electron transport, cytochrome c to oxygen / NADH dehydrogenase (ubiquinone) activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / midbrain development / electron transport chain / hypothalamus development / quinone binding / reactive oxygen species metabolic process / axon cytoplasm / aerobic respiration / cellular response to retinoic acid / respirasome / extrinsic apoptotic signaling pathway / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / hippocampus development / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / mitochondrial matrix / oxidoreductase activity / negative regulation of transcription, DNA-templated / protein-containing complex binding / mitochondrion / integral component of membrane / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Protein MGARP / Mitochondria Localisation Sequence / Protein MGARP, N-terminal / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit ...Protein MGARP / Mitochondria Localisation Sequence / Protein MGARP, N-terminal / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 protein / GRIM-19 / 2Fe-2S iron-sulfur cluster binding domain / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome c oxidase, subunit Va/VI superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / Cytochrome c oxidase subunit Va / NADH dehydrogenase 1 beta subcomplex subunit 2 / Cytochrome c oxidase, subunit Va/VI / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Globular protein, non-globular alpha/beta subunit / Thioredoxin-like [2Fe-2S] ferredoxin / Cytochrome b-c1 complex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH dehydrogenase subunit 2, C-terminal / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / Cytochrome b-c1 complex subunit 8 / UcrQ family / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge protein / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6, C-terminal / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c oxidase polypeptide Va / Ubiquinol-cytochrome c reductase core protein 1 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I-19kD / : / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / : / Complex I-AGGG ...NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c oxidase polypeptide Va / Ubiquinol-cytochrome c reductase core protein 1 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I-19kD / : / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / : / Complex I-AGGG / : / Complex I-15 kDa / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-PDSW / Complex I-B14.7 / Complex I-20kD / : / Complex I-B22 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / Complex I-B17 / Ubiquinol-cytochrome c reductase complex / Cytochrome b / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 3 / Complex I-MWFE / NADH-ubiquinone oxidoreductase chain 4 / : / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / CARDIOLIPIN / Complex I-B12 / Complex I-B9 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / IRON/SULFUR CLUSTER / Chem-ZMP / COPPER (II) ION / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex III subunit 8 / Rieske domain-containing protein / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Mitochondria localized glutamic acid rich protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / : / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-49kD / Cytochrome b-c1 complex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Uncharacterized protein / Acyl carrier protein / Complex I-MNLL / Cytochrome b-c1 complex subunit 10 / Complex I-SGDH / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsGu, J. / Wu, M. / Guo, R. / Yang, M.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0501100 and 2012CB911101 China
National Outstanding Young Scholar Science Foundation China
National Natural Science Foundation of China3162500065, 31030020 and 31170679 China
CitationJournal: Cell / Year: 2016
Title: Structure of Mammalian Respiratory Supercomplex IIIIIV.
Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang /
Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.
History
DepositionAug 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / em_image_scans / em_software / Item: _cell.Z_PDB / _em_software.name

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 6C
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
H: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
J: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
K: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
L: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
M: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
O: Acyl carrier protein, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
R: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
T: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: Acyl carrier protein, mitochondrial
Y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
b: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
c: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
e: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
f: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g: NADH dehydrogenase [ubiquinone] 1 subunit C2
h: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i: NADH-ubiquinone oxidoreductase chain 2
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
l: NADH-ubiquinone oxidoreductase chain 5
m: NADH-ubiquinone oxidoreductase chain 6
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
q: NADH-ubiquinone oxidoreductase chain 4
r: NADH-ubiquinone oxidoreductase chain 1
s: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
t: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
u: Cytochrome b-c1 complex subunit 1, mitochondrial
v: Cytochrome b-c1 complex subunit 2, mitochondrial
w: Cytochrome b
x: Cytochrome c1, heme protein, mitochondrial
y: Cytochrome b-c1 complex subunit 7
z: Cytochrome b-c1 complex subunit 8
0: Cytochrome b-c1 complex subunit 6, mitochondrial
1: Cytochrome b-c1 complex subunit 9
2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3: Cytochrome b-c1 complex subunit 10
4: Cytochrome b-c1 complex subunit Rieske, mitochondrial
5: Cytochrome b-c1 complex subunit 1, mitochondrial
6: Cytochrome b-c1 complex subunit 2, mitochondrial
7: Cytochrome b
8: Cytochrome c1, heme protein, mitochondrial
9: Cytochrome b-c1 complex subunit 7
Aa: Cytochrome b-c1 complex subunit 8
Ab: Cytochrome b-c1 complex subunit 6, mitochondrial
Ac: Cytochrome b-c1 complex subunit 9
Ad: Cytochrome b-c1 complex subunit 10
Ae: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Af: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Ag: Cytochrome c oxidase subunit 8B, mitochondrial
Ah: Cytochrome c oxidase subunit 7A1, mitochondrial
Ai: Cytochrome c oxidase subunit 7B, mitochondrial
Aj: Cytochrome c oxidase subunit 7C, mitochondrial
Ak: Cytochrome c oxidase subunit 1
Al: Cytochrome c oxidase subunit 2
Am: Cytochrome c oxidase subunit 3
An: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Ao: Cytochrome c oxidase subunit 5A, mitochondrial
Ap: Cytochrome c oxidase subunit 5B, mitochondrial
Aq: Cytochrome c oxidase subunit 6A, mitochondrial
Ar: Cytochrome c oxidase subunit 6B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,818,749132
Polymers1,781,94180
Non-polymers36,80852
Water0
1


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

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Components

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules AAgAhAiAjAkAlAmAnAoApAqAr

#1: Protein Cytochrome c oxidase subunit 6C /


Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#56: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial /


Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#57: Protein Cytochrome c oxidase subunit 7A1, mitochondrial /


Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#58: Protein Cytochrome c oxidase subunit 7B, mitochondrial /


Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#59: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial /


Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#60: Protein Cytochrome c oxidase subunit 1 /


Mass: 57065.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#61: Protein Cytochrome c oxidase subunit 2 /


Mass: 26040.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#62: Protein Cytochrome c oxidase subunit 3 /


Mass: 29943.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#63: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial /


Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#64: Protein Cytochrome c oxidase subunit 5A, mitochondrial /


Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#65: Protein Cytochrome c oxidase subunit 5B, mitochondrial /


Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#66: Protein Cytochrome c oxidase subunit 6A, mitochondrial /


Mass: 9452.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#67: Protein Cytochrome c oxidase subunit 6B1 /


Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules BE

#2: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RVN1
#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 26301.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SM98

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules CDFHIJh

#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial


Mass: 52552.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial


Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIF2
#6: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S031
#8: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 23893.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 23777.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LK43
#10: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 19718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6
#32: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23

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Protein , 4 types, 7 molecules GOXw7x8

#7: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHD7
#15: Protein Acyl carrier protein, mitochondrial


Mass: 17326.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAB6
#47: Protein Cytochrome b /


Mass: 42840.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#48: Protein Cytochrome c1, heme protein, mitochondrial /


Mass: 35488.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 13 molecules KRLMNPQSTUVWs

#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17162.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SA62
#14: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLY2
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RGE3
#17: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRG2
#18: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNI5
#20: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#21: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopt

#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial


Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRQ0
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3


Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SI50
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#26: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6


Mass: 15603.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21702.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#28: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LDC3
#29: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWV4
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1


Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SD73
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LPW0
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#44: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg

#30: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 8630.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRC9
#31: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1STY1

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmqr

#33: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79875
#34: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79880
#35: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P56632
#36: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9TDR1
#37: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#41: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79881
#42: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79874

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Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules u5v6y9zAa0Ab1Ac243AdAeAf

#45: Protein Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 52756.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKM0
#46: Protein Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48264.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#49: Protein Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#50: Protein Cytochrome b-c1 complex subunit 8


Mass: 9784.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI18
#51: Protein Cytochrome b-c1 complex subunit 6, mitochondrial


Mass: 10685.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S3W0
#52: Protein Cytochrome b-c1 complex subunit 9


Mass: 7412.530 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN79
#53: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 29492.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1
#54: Protein Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2
#55: Protein Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial


Mass: 7900.107 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1

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Non-polymers , 14 types, 52 molecules

#68: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#69: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#70: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#71: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM
#72: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#73: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#74: 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.: 10 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#75: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 749.073 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H83NO8P / Comment: DOPE, phospholipid*YM
#76: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#77: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#78: Chemical ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#79: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#80: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#81: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsTHE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE ...THE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE AUTHOR COULD OBSERVE SOME CONNECTED RESIDUES AND ASSIGNED UNK TO THESE RESIDUES. THE AUTHOR IS NOT SURE WHCIH PART OF RESIDUE 1-47 CORRESPONDS WITH THIS PEPTIDE OF UNK. SO THE RESIDUE NUMBERS OF UNK IS MEANINGLESS.

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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: Respiratory supercomplex I1III2IV1 / Type: COMPLEX / Details: Supercomplex generated by complex I, III and IV. / Entity ID: #1-#67 / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2image acquisition
4CTFFIND3CTF correction
7Coot0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.9model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161912 / Symmetry type: POINT

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