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- PDB-7d5i: Structure of Mycobacterium smegmatis bd complex in the apo-form. -

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Basic information

Entry
Database: PDB / ID: 7d5i
TitleStructure of Mycobacterium smegmatis bd complex in the apo-form.
Components
  • Cytochrome D ubiquinol oxidase subunit 1
  • Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
KeywordsOXIDOREDUCTASE / Mycobacterium smegmatis / electron transfer chain
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 / membrane => GO:0016020 / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME B/C / Cytochrome D ubiquinol oxidase subunit 1 / Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsWang, W. / Gong, H. / Gao, Y. / Zhou, X. / Rao, Z.
Funding support China, 3items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / em_entity_assembly_naturalsource
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism
Revision 1.2May 29, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral

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Structure visualization

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Assembly

Deposited unit
A: Cytochrome D ubiquinol oxidase subunit 1
B: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2205
Polymers93,3512
Non-polymers1,8693
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10950 Å2
ΔGint-126 kcal/mol
Surface area30200 Å2

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Components

#1: Protein Cytochrome D ubiquinol oxidase subunit 1


Mass: 53997.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_3233 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QXA8, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#2: Protein Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB


Mass: 39352.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: cydB, MSMEI_3150 / Production host: Escherichia coli (E. coli) / References: UniProt: I7GAS8, alkaline phosphatase
#3: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME / Heme


Mass: 632.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Mycobacterium smegmatis bd complex
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270938 / Details: The software used for reconstruction is cryoSPARC. / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066451
ELECTRON MICROSCOPYf_angle_d1.7828873
ELECTRON MICROSCOPYf_dihedral_angle_d11.1513569
ELECTRON MICROSCOPYf_chiral_restr0.044969
ELECTRON MICROSCOPYf_plane_restr0.0041085

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