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- PDB-9njb: hPNPase RNA pre-catalytic state -

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Basic information

Entry
Database: PDB / ID: 9njb
TitlehPNPase RNA pre-catalytic state
Components
  • Polyribonucleotide nucleotidyltransferase 1, mitochondrial
  • RNA (5'-R(P*AP*AP*UP*CP*UP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNase / Protein-RNA Complex / RNA degradation / mitochondria / phosphorolytic enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process / mitochondrial RNA 5'-end processing / poly(G) binding ...RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process / mitochondrial RNA 5'-end processing / poly(G) binding / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mitochondrial RNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / positive regulation of mRNA catabolic process / regulation of cellular senescence / rRNA import into mitochondrion / regulation of cellular respiration / response to growth hormone / RNA catabolic process / miRNA binding / poly(U) RNA binding / protein homotrimerization / mRNA catabolic process / response to cAMP / cellular response to interferon-beta / liver regeneration / mitochondrion organization / protein homooligomerization / mitochondrial intermembrane space / mRNA processing / cellular response to oxidative stress / 3'-5'-RNA exonuclease activity / ribosome / mitochondrial matrix / endoplasmic reticulum membrane / mitochondrion / RNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / 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
RNA / RNA (> 10) / Polyribonucleotide nucleotidyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsUnseld, O. / Das, H. / Hallberg, B.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Loop-mediated regulation and base flipping drive RNA cleavage by human mitochondrial PNPase
Authors: Unseld, O. / Das, H. / Hallberg, B.M.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
B: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
C: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
D: RNA (5'-R(P*AP*AP*UP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,2359
Polymers271,8994
Non-polymers3375
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase 1, mitochondrial / 3'-5' RNA exonuclease OLD35 / PNPase old-35 / Polynucleotide phosphorylase 1 / PNPase 1 / ...3'-5' RNA exonuclease OLD35 / PNPase old-35 / Polynucleotide phosphorylase 1 / PNPase 1 / Polynucleotide phosphorylase-like protein


Mass: 84417.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPT1, PNPASE / Plasmid: pDSG-103 / Cell line (production host): MEXi-293E / Production host: Homo sapiens (human)
References: UniProt: Q8TCS8, polyribonucleotide nucleotidyltransferase
#2: RNA chain RNA (5'-R(P*AP*AP*UP*CP*UP*A)-3')


Mass: 18647.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA ordered from IDT. / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Trimeric human PNPase bound to RNA in pre-catalytic state
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.258 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: MEXi-293E / Plasmid: pDSG-103
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
250 mMsodium chlorideNaCl1
32 mMmagnesium chlorideMgCl21
410 mMsodium sulfateNa2SO41
51 mMDTTditiotreitol1
60.1 mMsodium dihydrogen phosphateNaH2PO41
SpecimenConc.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 60s back side and 120s front side glow discharching
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 48.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4465

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.95model fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11RELION5.0-betaclassification
12cryoSPARC4.6.23D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178050 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 75.34 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingAccession code: AF-Q8TCS8-F1 / Chain residue range: 1-783 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.15 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214650
ELECTRON MICROSCOPYf_angle_d0.45219866
ELECTRON MICROSCOPYf_dihedral_angle_d8.252071
ELECTRON MICROSCOPYf_chiral_restr0.0422333
ELECTRON MICROSCOPYf_plane_restr0.0032551

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