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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | PNPase of Mycobacterium tuberculosis | |||||||||
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![]() | polynucleotide phosphorylase / Mycobacterium tuberculosis / RNA degradation / TRANSFERASE | |||||||||
Function / homology | : ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Wang N / Sheng YN / Liu YT | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of Mycobacterium tuberculosis polynucleotide phosphorylase suggest a potential mechanism for its RNA substrate degradation. Authors: Na Wang / Yanan Sheng / Yutong Liu / Yaoting Guo / Jun He / Jinsong Liu / ![]() Abstract: As one of the oldest infectious diseases in the world, tuberculosis (TB) is the second most deadly infectious disease after COVID-19. Tuberculosis is caused by Mycobacterium tuberculosis (Mtb), which ...As one of the oldest infectious diseases in the world, tuberculosis (TB) is the second most deadly infectious disease after COVID-19. Tuberculosis is caused by Mycobacterium tuberculosis (Mtb), which can attack various organs of the human body. Up to now, drug-resistant TB continues to be a public health threat. Pyrazinamide (PZA) is regarded as a sterilizing drug in the treatment of TB due to its distinct ability to target Mtb persisters. Previously we demonstrated that a D67N mutation in Mycobacterium tuberculosis polynucleotide phosphorylase (MtbPNPase, Rv2783c) confers resistance to PZA and Rv2783c is a potential target for PZA, but the mechanism leading to PZA resistance remains unclear. To gain further insight into the MtbPNPase, we determined the cryo-EM structures of apo Rv2783c, its mutant form and its complex with RNA. Our studies revealed the Rv2783c structure at atomic resolution and identified its enzymatic functional groups essential for its phosphorylase activities. We also investigated the molecular mechanisms underlying the resistance to PZA conferred by the mutation. Our research findings provide structural and functional insights enabling the development of new anti-tuberculosis drugs. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
Images | ![]() | 34 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 116.1 MB 116.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 884.2 KB | Display | ![]() |
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Full document | ![]() | 883.8 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wxfMC ![]() 8wwpC ![]() 8wx0C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37905_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37905_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : PNPase of Mycobacterium tuberculosis
Entire | Name: PNPase of Mycobacterium tuberculosis |
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Components |
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-Supramolecule #1: PNPase of Mycobacterium tuberculosis
Supramolecule | Name: PNPase of Mycobacterium tuberculosis / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Bifunctional guanosine pentaphosphate synthetase/polyribonucleoti...
Macromolecule | Name: Bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 82.117984 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MMSAAEIDEG VFETTATIDN GSFGTRTIRF ETGRLALQAA GAVVAYLDDD NMLLSATTAS KNPKEHFDF FPLTVDVEER MYAAGRIPGS FFRREGRPST DAILTCRLID RPLRPSFVDG LRNEIQIVVT ILSLDPGDLY D VLAINAAS ...String: MGSSHHHHHH SSGLVPRGSH MMSAAEIDEG VFETTATIDN GSFGTRTIRF ETGRLALQAA GAVVAYLDDD NMLLSATTAS KNPKEHFDF FPLTVDVEER MYAAGRIPGS FFRREGRPST DAILTCRLID RPLRPSFVDG LRNEIQIVVT ILSLDPGDLY D VLAINAAS ASTQLGGLPF SGPIGGVRVA LIDGTWVGFP TVDQIERAVF DMVVAGRIVE GDVAIMMVEA EATENVVELV EG GAQAPTE SVVAAGLEAA KPFIAALCTA QQELADAAGK SGKPTVDFPV FPDYGEDVYY SVSSVATDEL AAALTIGGKA ERD QRIDEI KTQVVQRLAD TYEGREKEVG AALRALTKKL VRQRILTDHF RIDGRGITDI RALSAEVAVV PRAHGSALFE RGET QILGV TTLDMIKMAQ QIDSLGPETS KRYMHHYNFP PFSTGETGRV GSPKRREIGH GALAERALVP VLPSVEEFPY AIRQV SEAL GSNGSTSMGS VCASTLALLN AGVPLKAPVA GIAMGLVSDD IQVEGAVDGV VERRFVTLTD ILGAEDAFGD MDFKVA GTK DFVTALQLDT KLDGIPSQVL AGALEQAKDA RLTILEVMAE AIDRPDEMSP YAPRVTTIKV PVDKIGEVIG PKGKVIN AI TEETGAQISI EDDGTVFVGA TDGPSAQAAI DKINAIANPQ LPTVGERFLG TVVKTTDFGA FVSLLPGRDG LVHISKLG K GKRIAKVEDV VNVGDKLRVE IADIDKRGKI SLILVADEDS TAAATDAATV TS UniProtKB: UNIPROTKB: A0A9Q6P703 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6.7 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: 50mM Tris, pH 8.0, 150 Nacl, 5mM DTT | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: OTHER Details: The value given for _em_vitrification.instrument is CRYOSOL VITROJET. This is not in a list of allowed values {'OTHER', 'FEI VITROBOT MARK IV', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'LEICA ...Details: The value given for _em_vitrification.instrument is CRYOSOL VITROJET. This is not in a list of allowed values {'OTHER', 'FEI VITROBOT MARK IV', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'LEICA KF80', 'GATAN CRYOPLUNGE 3', 'REICHERT-JUNG PLUNGER', 'SPOTITON', 'FEI VITROBOT MARK I', 'LEICA EM CPC', 'EMS-002 RAPID IMMERSION FREEZER', 'HOMEMADE PLUNGER', 'LEICA PLUNGER', 'FEI VITROBOT MARK II'} so OTHER is written into the XML file. | ||||||||||||
Details | protein sample was mixed with 15mM FOS-CHOLINE-8 (Anatrace) and rapidly loaded onto the holey carbon grids |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 2981 / Average exposure time: 1.6 sec. / Average electron dose: 2.22 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110060 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |