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- EMDB-11677: Cryo-EM structure of W107R after heme uptake (1heme molecule) Kat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11677 | |||||||||
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Title | Cryo-EM structure of W107R after heme uptake (1heme molecule) KatG from M. tuberculosis | |||||||||
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![]() | Heme / Peroxidase-Catalase / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / NADPH binding / positive regulation of DNA repair / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
![]() | Blundell TL / Chaplin AK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis. Authors: Asma Munir / Michael T Wilson / Steven W Hardwick / Dimitri Y Chirgadze / Jonathan A R Worrall / Tom L Blundell / Amanda K Chaplin / ![]() Abstract: Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding ...Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance. | |||||||||
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 | ![]() | 197.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.5 KB | Display | ![]() |
Images | ![]() | 11.8 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 194.4 MB 194.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a7cMC ![]() 6zjiC ![]() 7a2iC ![]() 7a7aC ![]() 7a8zC ![]() 7aa3C ![]() 7ag8C 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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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.652 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_11677_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_11677_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of W107R KatG after heme uptake from M. tuberculosis
Entire | Name: Cryo-EM structure of W107R KatG after heme uptake from M. tuberculosis |
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Components |
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-Supramolecule #1: Cryo-EM structure of W107R KatG after heme uptake from M. tuberculosis
Supramolecule | Name: Cryo-EM structure of W107R KatG after heme uptake from M. tuberculosis type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 161.1 kDa/nm |
-Macromolecule #1: Catalase-peroxidase
Macromolecule | Name: Catalase-peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: catalase-peroxidase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 80.658594 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPEQHPPITE TTTGAASNGC PVVGHMKYPV EGGGNQDWWP NRLNLKVLHQ NPAVADPMGA AFDYAAEVAT IDVDALTRDI EEVMTTSQP WWPADYGHYG PLFIRMARHA AGTYRIHDGR GGAGGGMQRF APLNSWPDNA SLDKARRLLW PVKKKYGKKL S WADLIVFA ...String: MPEQHPPITE TTTGAASNGC PVVGHMKYPV EGGGNQDWWP NRLNLKVLHQ NPAVADPMGA AFDYAAEVAT IDVDALTRDI EEVMTTSQP WWPADYGHYG PLFIRMARHA AGTYRIHDGR GGAGGGMQRF APLNSWPDNA SLDKARRLLW PVKKKYGKKL S WADLIVFA GNCALESMGF KTFGFGFGRV DQWEPDEVYW GKEATWLGDE RYSGKRDLEN PLAAVQMGLI YVNPEGPNGN PD PMAAAVD IRETFRRMAM NDVETAALIV GGHTFGKTHG AGPADLVGPE PEAAPLEQMG LGWKSSYGTG TGKDAITSGI EVV WTNTPT KWDNSFLEIL YGYEWELTKS PAGAWQYTAK DGAGAGTIPD PFGGPGRSPT MLATDLSLRV DPIYERITRR WLEH PEELA DEFAKAWYKL IHRDMGPVAR YLGPLVPKQT LLWQDPVPAV SHDLVGEAEI ASLKSQIRAS GLTVSQLVST AWAAA SSFR GSDKRGGANG GRIRLQPQVG WEVNDPDGDL RKVIRTLEEI QESFNSAAPG NIKVSFADLV VLGGCAAIEK AAKAAG HNI TVPFTPGRTD ASQEQTDVES FAVLEPKADG FRNYLGKGNP LPAEYMLLDK ANLLTLSAPE MTVLVGGLRV LGANYKR LP LGVFTEASES LTNDFFVNLL DMGITWEPSP ADDGTYQGKD GSGKVKWTGS RVDLVFGSNS ELRALVEVYG ADDAQPKF V QDFVAAWDKV MNLDRFDVR UniProtKB: Catalase-peroxidase |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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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) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 244867 / Average electron dose: 39.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |