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- EMDB-21897: The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-21897
TitleThe Cryo-EM structure of the ubiquinol oxidase from Escherichia coli
Map data
Sampleubiquinol oxidase
  • (Cytochrome o ubiquinol oxidase, subunit ...) x 2
  • Ubiquinol oxidase subunit 2
  • Cytochrome o ubiquinol oxidase
  • (ligand) x 6
Function / homology
Function and homology information


ubiquinol oxidase (H+-transporting) / cytochrome o ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / aerobic respiration / respirasome / copper ion binding / heme binding ...ubiquinol oxidase (H+-transporting) / cytochrome o ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / aerobic respiration / respirasome / copper ion binding / heme binding / integral component of membrane / plasma membrane
COX aromatic rich motif / Cytochrome o ubiquinol oxidase, subunit I / Cytochrome o ubiquinol oxidase, subunit III / Cupredoxin / Cytochrome o ubiquinol oxidase subunit II / Cytochrome C oxidase subunit IV, prokaryotes / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit III-like / Cytochrome o ubiquinol oxidase subunit IV ...COX aromatic rich motif / Cytochrome o ubiquinol oxidase, subunit I / Cytochrome o ubiquinol oxidase, subunit III / Cupredoxin / Cytochrome o ubiquinol oxidase subunit II / Cytochrome C oxidase subunit IV, prokaryotes / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit III-like / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit III / Ubiquinol oxidase subunit III domain / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C oxidase subunit II, transmembrane domain
Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsSu C-C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 2, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wti
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21897.png

Downloads & links

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Map

FileDownload / File: emd_21897.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 106 pix.
= 114.48 Å		1.08 Å/pix.
x 85 pix.
= 91.8 Å		1.08 Å/pix.
x 97 pix.
= 104.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-3.6237965 - 6.270592
Average (Standard dev.)-7.136194e-12 (±0.41026497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin10810495
Dimensions8597106
Spacing1068597
CellA: 114.48 Å / B: 91.8 Å / C: 104.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z1068597
origin x/y/z0.0000.0000.000
length x/y/z114.48091.800104.760
α/β/γ90.00090.00090.000
start NX/NY/NZ95108104
NX/NY/NZ1068597
MAP C/R/S321
start NC/NR/NS10410895
NC/NR/NS9785106
D min/max/mean-3.6246.271-0.000

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Supplemental data

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Additional map: #1

Fileemd_21897_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire ubiquinol oxidase

EntireName: ubiquinol oxidase / Number of components: 11

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Component #1: protein, ubiquinol oxidase

ProteinName: ubiquinol oxidase / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Cytochrome o ubiquinol oxidase, subunit I

ProteinName: Cytochrome o ubiquinol oxidase, subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.424469 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Ubiquinol oxidase subunit 2

ProteinName: Ubiquinol oxidase subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.947203 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Cytochrome o ubiquinol oxidase

ProteinName: Cytochrome o ubiquinol oxidase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.642566 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Cytochrome o ubiquinol oxidase, subunit IV

ProteinName: Cytochrome o ubiquinol oxidase, subunit IV / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.037402 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #7: ligand, HEME O

LigandName: HEME O / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.838854 kDa

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Component #8: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

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Component #9: ligand, Ubiquinone-8

LigandName: Ubiquinone-8Coenzyme Q10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.727109 kDa

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Component #10: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Component #11: ligand, pentadecyl(tetradecyl)peroxyanhydride

LigandName: pentadecyl(tetradecyl)peroxyanhydride / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.524859 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 334222
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6wti

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