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- EMDB-30582: Structure of Mycobacterium smegmatis bd complex in the apo-form. -

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Basic information

Entry
Database: EMDB / ID: EMD-30582
TitleStructure of Mycobacterium smegmatis bd complex in the apo-form.
Map data
Sample
  • Complex: Cryo-EM structure of Mycobacterium smegmatis bd complex
    • Protein or peptide: Cytochrome D ubiquinol oxidase subunit 1
    • Protein or peptide: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
KeywordsMycobacterium smegmatis / electron transfer chain / Oxidoreductase
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 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsWang W / 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
DepositionSep 26, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / 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
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  • 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-7d5i
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30582.png

Downloads & links

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Map

FileDownload / File: emd_30582.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: 0.7
Minimum - Maximum-2.2122407 - 3.9668531
Average (Standard dev.)0.00079936656 (±0.15904944)
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
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.2123.9670.001

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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
    • Protein or peptide: Cytochrome D ubiquinol oxidase subunit 1
    • Protein or peptide: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
  • Ligand: HEME B/C
  • Ligand: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

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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 155 (bacteria)

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Macromolecule #1: Cytochrome D ubiquinol oxidase subunit 1

MacromoleculeName: Cytochrome D ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 53.997961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDALDLSRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTVWV ATGNDTWYRL TRFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD IFGAPLAMEG LAAFFFESTF IGLWIFGWTR LPRWLHLACI WIVAIAVNLS AFFIISANSF MQHPVGARFN P ETGRAELE ...String:
MDALDLSRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTVWV ATGNDTWYRL TRFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD IFGAPLAMEG LAAFFFESTF IGLWIFGWTR LPRWLHLACI WIVAIAVNLS AFFIISANSF MQHPVGARFN P ETGRAELE SIFALFTNNT AIAAFTHAVS GAFLTAGVFV ACVCAWWMVR SHRTGGESAA DAATMYRPAT ILGCWVTLVA AV ALFFTGD AQGKLMFEQQ PMKMASAESL CHSEQDPSFS VLTVGTHNNC DSVVHLIEVP YVLPFLAEGK FSGVHLDGVV DLQ RSYEEK FGPGDYRPNL FVTYWSFRAM IGFLAVPGLF ALAALWLTRG GRIPDQRWFS WFALLTIPTP FLANSAGWVF TEMG RQPWV VVPNPTGDQD IRLTVAQGVS DHSVGLVVLS LVAFTLVYAV LAVIWFFLLR RYIVQGPSEH DSEPAAPRPP DADDV APLS FAY

UniProtKB: Cytochrome D ubiquinol oxidase subunit 1

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Macromolecule #2: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB

MacromoleculeName: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: alkaline phosphatase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 39.35266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLQELWFIL LAVLFLGFFL LEGFDFGVGM LMSFFGRAAE KRGQDPEPYR RAALNTIGPV WDGNEVWLIT AGGAMFAAFP EMYASMFSG LYLALLVILC AMILRIVAIE WRGKIDDPGW RRWADTGIAV GSWVPAILWG VAFASLVRGL PVDADKQIHL S FFGDLLNA ...String:
MGLQELWFIL LAVLFLGFFL LEGFDFGVGM LMSFFGRAAE KRGQDPEPYR RAALNTIGPV WDGNEVWLIT AGGAMFAAFP EMYASMFSG LYLALLVILC AMILRIVAIE WRGKIDDPGW RRWADTGIAV GSWVPAILWG VAFASLVRGL PVDADKQIHL S FFGDLLNA YTLLGGLATC ALFAFHGAVF VSLKTSGEIR TDAFGFARLL ALPATALVAA FGVWTQVAHG TGWTWIVLAA AV IAQLVAV AQVFRGSGEG WAFGATSVVV AAVVVLLFGS LFPDLIPSTL NPDWSLTIYN GSSSPYTLKI MTWAALVFAP LVV VYQGWT YWVFSKRISA DRIPAPIGLS RRSSHHHHHH HHHH

UniProtKB: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB

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Macromolecule #3: HEME B/C

MacromoleculeName: HEME B/C / type: ligand / ID: 3 / Number of copies: 2 / Formula: HEB
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEB:
HEME B/C

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Macromolecule #4: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

MacromoleculeName: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HDD
Molecular weightTheoretical: 632.487 Da
Chemical component information

ChemComp-HDD:
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE

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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 K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: The software used for reconstruction is cryoSPARC. / Number images used: 270938
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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