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- PDB-6hwh: Structure of a functional obligate respiratory supercomplex from ... -

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Entry
Database: PDB / ID: 6hwh
TitleStructure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Components
  • (Co-purified unknown peptide built as ...) x 2
  • (Co-purified unknown transmembrane helices built as ...) x 2
  • (Cytochrome c oxidase subunit ...) x 3
  • (Ubiquinol-cytochrome ...) x 2
  • Cytochrome bc1 complex cytochrome c subunit
  • Cytochrome c oxidase polypeptide 4
  • MSMEG_4693
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
KeywordsELECTRON TRANSPORT / Membrane Protein / Cryo-EM / Respiratory supercomplex / Mycobacterium
Function / homologyCytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c-like domain / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase, subunit I bacterial type / Rieske iron-sulphur protein / Di-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome c oxidase subunit IV, actinobacteria ...Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c-like domain / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase, subunit I bacterial type / Rieske iron-sulphur protein / Di-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome c oxidase subunit IV, actinobacteria / Rieske [2Fe-2S] domain / Cytochrome b/b6, N-terminal / Cytochrome c oxidase subunit III / Cytochrome b/b6-like domain superfamily / Protein of unknown function DUF5130 / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c-like domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c oxidase-like, subunit I superfamily / Cupredoxin / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome C oxidase subunit II, periplasmic domain / Copper centre Cu(A) / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c family profile. / Cytochrome b/b6 N-terminal region profile. / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome oxidase subunit I profile. / Heme-copper oxidase subunit III family profile. / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C and Quinol oxidase polypeptide I / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Domain of unknown function (DUF5130) / Cytochrome b(N-terminal)/b6/petB / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase subunit I / oxidoreductase activity, acting on diphenols and related substances as donors / electron transport coupled proton transport / oxidative phosphorylation / ubiquinol—cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / aerobic electron transport chain / cytochrome-c oxidase / cytochrome-c oxidase activity / respiratory electron transport chain / aerobic respiration / respirasome / 2 iron, 2 sulfur cluster binding / copper ion binding / iron ion binding / heme binding / integral component of membrane / plasma membrane / metal ion binding / Cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome c oxidase polypeptide 4 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 1 / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / Ubiquinol-cytochrome C reductase QcrB
Function and homology information
Specimen sourceMycobacterium smegmatis MC2 155 (bacteria)
Mycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsWiseman, B. / Nitharwal, R.G. / Fedotovskaya, O. / Schafer, J. / Guo, H. / Kuang, Q. / Benlekbir, S. / Sjostrand, D. / Adelroth, P. / Rubinstein, J.L. / Brzezinski, P. / Hogbom, M.
CitationJournal: To Be Published
Title: Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Authors: Wiseman, B. / Nitharwal, R.G. / Fedotovskaya, O. / Schafer, J. / Guo, H. / Kuang, Q. / Benlekbir, S. / Sjostrand, D. / Adelroth, P. / Rubinstein, J.L. / Brzezinski, P. / Hogbom, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2018 / Release: Nov 7, 2018

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Structure visualization

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  • Biological unit as author_and_software_defined_assembly
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  • Deposited structure unit
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Assembly

Deposited unit
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Co-purified unknown transmembrane helices built as polyALA
H: Co-purified unknown transmembrane helices built as polyALA
I: Co-purified unknown peptide built as polyALA
J: Co-purified unknown peptide built as polyALA
M: Cytochrome bc1 complex cytochrome c subunit
P: Cytochrome c oxidase subunit 2
R: MSMEG_4693
T: Uncharacterized protein MSMEG_4692/MSMEI_4575
V: Cytochrome c oxidase subunit 1
X: Cytochrome c oxidase polypeptide 4
Z: Cytochrome c oxidase subunit 3
b: Ubiquinol-cytochrome C reductase QcrB
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
C: Co-purified unknown transmembrane helices built as polyALA
D: Co-purified unknown transmembrane helices built as polyALA
E: Co-purified unknown peptide built as polyALA
F: Co-purified unknown peptide built as polyALA
K: Cytochrome bc1 complex cytochrome c subunit
L: Cytochrome c oxidase subunit 2
N: MSMEG_4693
O: Uncharacterized protein MSMEG_4692/MSMEI_4575
Q: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase polypeptide 4
W: Cytochrome c oxidase subunit 3
Y: Ubiquinol-cytochrome C reductase QcrB
i: Cytochrome bc1 complex cytochrome c subunit
j: Cytochrome bc1 complex cytochrome c subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,29660
Polyers686,08628
Non-polymers24,21032
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis, microscopy, negative staining and cryo
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
2
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Co-purified unknown transmembrane helices built as polyALA
H: Co-purified unknown transmembrane helices built as polyALA
I: Co-purified unknown peptide built as polyALA
J: Co-purified unknown peptide built as polyALA
M: Cytochrome bc1 complex cytochrome c subunit
P: Cytochrome c oxidase subunit 2
R: MSMEG_4693
T: Uncharacterized protein MSMEG_4692/MSMEI_4575
V: Cytochrome c oxidase subunit 1
X: Cytochrome c oxidase polypeptide 4
Z: Cytochrome c oxidase subunit 3
b: Ubiquinol-cytochrome C reductase QcrB
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
C: Co-purified unknown transmembrane helices built as polyALA
D: Co-purified unknown transmembrane helices built as polyALA
E: Co-purified unknown peptide built as polyALA
F: Co-purified unknown peptide built as polyALA
K: Cytochrome bc1 complex cytochrome c subunit
L: Cytochrome c oxidase subunit 2
N: MSMEG_4693
O: Uncharacterized protein MSMEG_4692/MSMEI_4575
Q: Cytochrome c oxidase subunit 1
S: Cytochrome c oxidase polypeptide 4
W: Cytochrome c oxidase subunit 3
Y: Ubiquinol-cytochrome C reductase QcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,69155
Polyers630,33626
Non-polymers22,35429
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)157740
ΔGint (kcal/M)-1432
Surface area (Å2)170610
MethodPISA

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Components

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Ubiquinol-cytochrome ... , 2 types, 4 molecules ABbY

#1: Protein/peptide Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 44869.395 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R051
#13: Protein/peptide Ubiquinol-cytochrome C reductase QcrB


Mass: 61271.945 Da / Num. of mol.: 2
Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria)
Gene: qcrB, MSMEI_4163 / Production host: Mycobacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FGS8, ubiquinol—cytochrome-c reductase

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Co-purified unknown transmembrane helices built as ... , 2 types, 4 molecules GCHD

#2: Protein/peptide Co-purified unknown transmembrane helices built as polyALA


Mass: 6315.777 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)
#3: Protein/peptide Co-purified unknown transmembrane helices built as polyALA


Mass: 5549.833 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)

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Co-purified unknown peptide built as ... , 2 types, 4 molecules IEJF

#4: Protein/peptide Co-purified unknown peptide built as polyALA


Mass: 1720.111 Da / Num. of mol.: 2
Details: chains M,K: transmembrane helix built and refined to density. chains i, j: homology model of ...chains M,K: transmembrane helix built and refined to density. chains i, j: homology model of soluble domain built as polyALA only rigid-body docked to density.
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)
#5: Protein/peptide Co-purified unknown peptide built as polyALA


Mass: 2996.685 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis MC2 155 (bacteria)

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Protein/peptide , 4 types, 10 molecules MKijRNTOXS

#6: Protein/peptide
Cytochrome bc1 complex cytochrome c subunit


Mass: 27874.547 Da / Num. of mol.: 4
Details: chains M,K: transmembrane helix built and refined into density chains i,j: homology model of the ...chains M,K: transmembrane helix built and refined into density chains i,j: homology model of the periplasmic soluble domain built as polyALA and rigid-body docked into low resolution density
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R050, ubiquinol—cytochrome-c reductase
#8: Protein/peptide MSMEG_4693


Mass: 8365.549 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R1B6
#9: Protein/peptide Uncharacterized protein MSMEG_4692/MSMEI_4575


Mass: 15910.971 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R1B5
#11: Protein/peptide Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15177.424 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R056, cytochrome-c oxidase

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

#7: Protein/peptide Cytochrome c oxidase subunit 2 /


Mass: 38077.465 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R057, cytochrome-c oxidase
#10: Protein/peptide Cytochrome c oxidase subunit 1 /


Mass: 64841.637 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R0M4, cytochrome-c oxidase
#12: Protein/peptide Cytochrome c oxidase subunit 3 /


Mass: 22196.883 Da / Num. of mol.: 2
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
References: UniProt: A0R049, cytochrome-c oxidase

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Non-polymers , 7 types, 32 molecules

#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#15: 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.: 8 / Formula: C81H156O17P2 / Cardiolipin / Comment: phospholipid *YM
#16: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 4 / Formula: C56H80O2
#17: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Formula: Cu / Copper
#18: Chemical
ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 4 / Formula: C54H64FeN4O6
#19: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Formula: C34H34FeN4O4 / Heme C
#20: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Respiratory Supercomplex from Mycobacterium smegmatis / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13 / Source: NATURAL
Molecular weightValue: 0.770 MDa / Experimental value: YES
Source (natural)Cellular location: membrane / Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: deletion of the complex III operon qcrCAB (qcrCAB::hyg)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 40 seconds at 20 mA / Grid material: COPPER / Grid mesh size: 300
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 5316

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Coot0.8.9.1model fitting
8UCSF Chimera1.11.2model fitting
10Coot0.8.9.1model refinement
11PHENIX1.14-3228-000model refinement
13cryoSPARC2final Euler assignment
14cryoSPARC2classification
15cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 751329
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 104198 / Symmetry type: POINT
Atomic model buildingDetails: Model was built de novo; except for chains i,j which are polyALA homology models rigid-body docked into low resolution density.
Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation coefficient

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