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- EMDB-30582: Structure of Mycobacterium smegmatis bd complex in the apo-form. -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30582 | ||||||||||||
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Title | Structure of Mycobacterium smegmatis bd complex in the apo-form. | ||||||||||||
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![]() | Mycobacterium smegmatis / electron transfer chain / Oxidoreductase | ||||||||||||
Function / homology | ![]() Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / cytochrome complex / alkaline phosphatase / alkaline phosphatase activity / aerobic electron transport chain / membrane => GO:0016020 / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | ||||||||||||
![]() | Wang W / Gong H | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 33.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 169 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 637.5 KB | Display | ![]() |
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Full document | ![]() | 637.1 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d5iMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of Mycobacterium smegmatis bd complex
Entire | Name: Cryo-EM structure of Mycobacterium smegmatis bd complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of Mycobacterium smegmatis bd complex
Supramolecule | Name: Cryo-EM structure of Mycobacterium smegmatis bd complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Cytochrome D ubiquinol oxidase subunit 1
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.997961 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.35266 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: HEME B/C
Macromolecule | Name: HEME B/C / type: ligand / ID: 3 / Number of copies: 2 / Formula: HEB |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ![]() ChemComp-HEB: |
-Macromolecule #4: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
Macromolecule | Name: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HDD |
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Molecular weight | Theoretical: 632.487 Da |
Chemical component information | ![]() ChemComp-HDD: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 model | Type of model: NONE |
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Final reconstruction | Resolution.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 assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |