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- EMDB-0289: Structure of a functional obligate respiratory supercomplex from ... -

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Entry
Database: EMDB / ID: 0289
TitleStructure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Map dataRespiratory supercomplex from Mycobacterium smegmatis
SampleRespiratory Supercomplex from Mycobacterium smegmatis
  • (Ubiquinol-cytochrome ...) x 2
  • (Co-purified unknown transmembrane helices built as ...) x 2
  • (Co-purified unknown peptide built as ...) x 2
  • Cytochrome bc1 complex cytochrome c subunit
  • (Cytochrome c oxidase subunit ...) x 3
  • MSMEG_4693
  • Uncharacterized protein MSMEG_4692/MSMEI_4575
  • Cytochrome c oxidase polypeptide 4
  • (ligand) x 7
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 / respiratory chain / 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
SourceMycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Mycobacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsWiseman B / Nitharwal RG / Fedotovskaya O / Schafer J / Guo H / Kuang Q / Benlekbir S / Sjostrand D / Adelroth P / Rubinstein JL / Brzezinski P / Hogbom M
CitationJournal: To Be Published
Title: Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Authors: Wiseman B / Nitharwal RG / Fedotovskaya O / Schafer J / Guo H / Kuang Q / Benlekbir S / Sjostrand D / Adelroth P / Rubinstein JL / Brzezinski P / Hogbom M
Validation ReportPDB-ID: 6hwh

SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.475
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.475
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hwh
  • Surface level: 0.475
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0289.map.gz (map file in CCP4 format, 219489 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
380 pix
1.06 Å/pix.
= 402.8 Å
380 pix
1.06 Å/pix.
= 402.8 Å
380 pix
1.06 Å/pix.
= 402.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.475 (by author), 0.475 (movie #1):
Minimum - Maximum-3.9200296 - 5.8836565
Average (Standard dev.)0.009659335 (0.12999378)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions380380380
Origin0.00.00.0
Limit379.0379.0379.0
Spacing380380380
CellA=B=C: 402.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z402.800402.800402.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-3.9205.8840.010

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Supplemental data

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Sample components

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Entire Respiratory Supercomplex from Mycobacterium smegmatis

EntireName: Respiratory Supercomplex from Mycobacterium smegmatis / Number of components: 21

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Component #1: protein, Respiratory Supercomplex from Mycobacterium smegmatis

ProteinName: Respiratory Supercomplex from Mycobacterium smegmatis / Recombinant expression: No
MassExperimental: 770 kDa
SourceSpecies: Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: deletion of the complex III operon qcrCAB (qcrCAB::hyg)

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Component #2: protein, Ubiquinol-cytochrome c reductase iron-sulfur subunit

ProteinName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.869395 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #3: protein, Co-purified unknown transmembrane helices built as polyALA

ProteinName: Co-purified unknown transmembrane helices built as polyALA
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.315777 kDa
SourceSpecies: Mycobacterium smegmatis MC2 155 (bacteria)

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Component #4: protein, Co-purified unknown transmembrane helices built as polyALA

ProteinName: Co-purified unknown transmembrane helices built as polyALA
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 5.549833 kDa
SourceSpecies: Mycobacterium smegmatis MC2 155 (bacteria)

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Component #5: protein, Co-purified unknown peptide built as polyALA

ProteinName: Co-purified unknown peptide built as polyALA
Details: 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.
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.720111 kDa
SourceSpecies: Mycobacterium smegmatis MC2 155 (bacteria)

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Component #6: protein, Co-purified unknown peptide built as polyALA

ProteinName: Co-purified unknown peptide built as polyALA / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.996685 kDa
SourceSpecies: Mycobacterium smegmatis MC2 155 (bacteria)

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Component #7: protein, Cytochrome bc1 complex cytochrome c subunit

ProteinName: Cytochrome bc1 complex cytochrome c subunit
Details: 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
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 27.874547 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #8: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 38.077465 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #9: protein, MSMEG_4693

ProteinName: MSMEG_4693 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.365549 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #10: protein, Uncharacterized protein MSMEG_4692/MSMEI_4575

ProteinName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.910971 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #11: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 64.841637 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #12: protein, Cytochrome c oxidase polypeptide 4

ProteinName: Cytochrome c oxidase polypeptide 4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.177424 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #13: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.196883 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)

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Component #14: protein, Ubiquinol-cytochrome C reductase QcrB

ProteinName: Ubiquinol-cytochrome C reductase QcrB / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 61.271945 kDa
SourceSpecies: Mycobacterium smegmatis MC2 155 (bacteria)
Source (engineered)Expression System: Mycobacterium smegmatis MC2 155 (bacteria)

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Component #15: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #16: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

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Component #17: ligand, MENAQUINONE-9

LigandName: MENAQUINONE-9Vitamin K2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.785233 kDa

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Component #18: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

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Component #19: ligand, HEME-AS

LigandName: HEME-AS / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.920954 kDa

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Component #20: ligand, HEME C

LigandName: HEME C / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.618503 kDa

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Component #21: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.5
Support film40 seconds at 20 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 43 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5316

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 104198
3D reconstructionSoftware: cryoSPARC / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL
Details: Model was built de novo; except for chains i,j which are polyALA homology models rigid-body docked into low resolution density.
Output model

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