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- EMDB-31302: Cryo-EM map of Mycobacterium smegmatis bd complex pre-incubated w... -

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Basic information

Entry
Database: EMDB / ID: EMD-31302
TitleCryo-EM map of Mycobacterium smegmatis bd complex pre-incubated with aurachin D(AD)
Map data
Sample
  • Complex: Cryo-EM structure of Mycobacterium smegmatis bd complex
Function / homology
Function and homology information


Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / cytochrome complex / alkaline phosphatase / alkaline phosphatase activity / aerobic electron transport chain / electron transfer activity / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
Cytochrome D ubiquinol oxidase subunit 1 / Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 51 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsWang W / Gao Y / Zhou X / Wang Q / Rao Z / Gong H
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030201, XDB37020203 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels.
Authors: Weiwei Wang / Yan Gao / Yanting Tang / Xiaoting Zhou / Yuezheng Lai / Shan Zhou / Yuying Zhang / Xiuna Yang / Fengjiang Liu / Luke W Guddat / Quan Wang / Zihe Rao / Hongri Gong /
Abstract: Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the ...Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase.
History
DepositionMay 13, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31302.png

Downloads & links

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Map

FileDownload / File: emd_31302.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.8
Minimum - Maximum-5.540678 - 6.425146
Average (Standard dev.)0.0028812513 (±0.16688968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z209.920209.920209.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-5.5416.4250.003

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Mycobacterium smegmatis bd complex

EntireName: Cryo-EM structure of Mycobacterium smegmatis bd complex
Components
  • Complex: Cryo-EM structure of Mycobacterium smegmatis bd complex

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Supramolecule #1: Cryo-EM structure of Mycobacterium smegmatis bd complex

SupramoleculeName: Cryo-EM structure of Mycobacterium smegmatis bd complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria)
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 51 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 158610
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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