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- EMDB-51455: Mtb PNPase Rv2783c Mutant L328F -

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Basic information

Entry
Database: EMDB / ID: EMD-51455
TitleMtb PNPase Rv2783c Mutant L328F
Map data
Sample
  • Complex: gpsI Mycobacterium tuberculosis polynucleotide phosphorylase
    • Complex: Polyribonucleotide nucleotidyltransferase
      • Protein or peptide: Polyribonucleotide nucleotidyltransferase
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: 1-[[4-[4-[[2-phenyl-5-(trifluoromethyl)-1,3-oxazol-4-yl]carbonylamino]phenyl]phenyl]carbonylamino]cyclopentane-1-carboxylic acid
KeywordsPNPase / GpsI / RNA Degradosome / PNPase Inhibitor / RNA
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / RNA catabolic process / mRNA catabolic process / RNA processing / peptidoglycan-based cell wall / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / plasma membrane / cytosol
Similarity search - Function
Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain ...Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsGriesser T / Sander P
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_197699/1 Switzerland
CitationJournal: To Be Published
Title: Identification, enzymatic and structural characterization of Mycobacterium tuberculosis PNPase (Rv2783c) as novel drug target
Authors: Griesser T / Sander P
History
DepositionAug 29, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51455.png

Downloads & links

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Map

FileDownload / File: emd_51455.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.24551776 - 0.7187902
Average (Standard dev.)-0.00065811473 (±0.01620637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51455_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51455_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : gpsI Mycobacterium tuberculosis polynucleotide phosphorylase

EntireName: gpsI Mycobacterium tuberculosis polynucleotide phosphorylase
Components
  • Complex: gpsI Mycobacterium tuberculosis polynucleotide phosphorylase
    • Complex: Polyribonucleotide nucleotidyltransferase
      • Protein or peptide: Polyribonucleotide nucleotidyltransferase
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: 1-[[4-[4-[[2-phenyl-5-(trifluoromethyl)-1,3-oxazol-4-yl]carbonylamino]phenyl]phenyl]carbonylamino]cyclopentane-1-carboxylic acid

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Supramolecule #1: gpsI Mycobacterium tuberculosis polynucleotide phosphorylase

SupramoleculeName: gpsI Mycobacterium tuberculosis polynucleotide phosphorylase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Mycobacterium tuberculosis polynucleotide phosphorylase
Molecular weightTheoretical: 0.119 kDa/nm

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Supramolecule #2: Polyribonucleotide nucleotidyltransferase

SupramoleculeName: Polyribonucleotide nucleotidyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Polyribonucleotide nucleotidyltransferase

MacromoleculeName: Polyribonucleotide nucleotidyltransferase / type: protein_or_peptide / ID: 1 / Details: Mutant L328F / Number of copies: 3 / Enantiomer: LEVO / EC number: polyribonucleotide nucleotidyltransferase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 63.441617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEIDEGVFET TATIDNGSFG TRTIRFETGR LALQAAGAVV AYLDDDNMLL SATTASKNPK EHFDFFPLTV DVEERMYAAG RIPGSFFRR EGRPSTDAIL TCRLIDRPLR PSFVDGLRNE IQIVVTILSL DPGDLYDVLA INAASASTQL GGLPFSGPIG G VRVALIDG ...String:
AEIDEGVFET TATIDNGSFG TRTIRFETGR LALQAAGAVV AYLDDDNMLL SATTASKNPK EHFDFFPLTV DVEERMYAAG RIPGSFFRR EGRPSTDAIL TCRLIDRPLR PSFVDGLRNE IQIVVTILSL DPGDLYDVLA INAASASTQL GGLPFSGPIG G VRVALIDG TWVGFPTVDQ IERAVFDMVV AGRIVEGDVA IMMVEAEATE NVVELVEGGA QAPTESVVAA GLEAAKPFIA AL CTAQQEL ADAAGKSGKP TVDFPVFPDY GEDVYYSVSS VATDELAAAL TIGGKAERDQ RIDEIKTQVV QRLADTYEGR EKE VGAAFR ALTKKLVRQR ILTDHFRIDG RGITDIRALS AEVAVVPRAH GSALFERGET QILGVTTLDM IKMAQQIDSL GPET SKRYM HHYNFPPFST GETGRVGSPK RREIGHGALA ERALVPVLPS VEEFPYAIRQ VSEALGSNGS TSMGSVCAST LALLN AGVP LKAPVAGIAM GLVSDDIQVE GAVDGVVERR FVTLTDILGA EDAFGDMDFK VAGTKDFVTA LQLDTKLDGI PSQVLA GAL EQAKDARLTI LEVMAEAIDR PDEMSPYAPR

UniProtKB: Polyribonucleotide nucleotidyltransferase

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Macromolecule #2: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 4.89313 KDa
SequenceString:
AAAAAAAAAA AAAAA

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Macromolecule #3: 1-[[4-[4-[[2-phenyl-5-(trifluoromethyl)-1,3-oxazol-4-yl]carbonyla...

MacromoleculeName: 1-[[4-[4-[[2-phenyl-5-(trifluoromethyl)-1,3-oxazol-4-yl]carbonylamino]phenyl]phenyl]carbonylamino]cyclopentane-1-carboxylic acid
type: ligand / ID: 3 / Number of copies: 3 / Formula: A1IM2
Molecular weightTheoretical: 563.524 Da

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 6.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1264862
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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