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- PDB-5zf6: Crystal structure of the dimeric human PNPase -

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Basic information

Entry
Database: PDB / ID: 5zf6
TitleCrystal structure of the dimeric human PNPase
ComponentsPolyribonucleotide nucleotidyltransferase 1, mitochondrialPolynucleotide phosphorylase
KeywordsTRANSFERASE / dimeric human PNPase
Function / homology
Function and homology information


RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial RNA 5'-end processing / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process ...RNA import into mitochondrion / mitochondrial mRNA polyadenylation / mitochondrial RNA 5'-end processing / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / poly(G) binding / nuclear polyadenylation-dependent mRNA catabolic process / positive regulation of mRNA catabolic process / regulation of cellular senescence / negative regulation of growth / rRNA import into mitochondrion / regulation of cellular respiration / RNA catabolic process / response to growth hormone / poly(U) RNA binding / miRNA binding / mRNA catabolic process / protein homotrimerization / cellular response to interferon-beta / response to cAMP / mitochondrion organization / liver regeneration / protein homooligomerization / mitochondrial intermembrane space / mRNA processing / cellular response to oxidative stress / 3'-5'-RNA exonuclease activity / regulation of cell cycle / ribosome / mitochondrial matrix / endoplasmic reticulum membrane / mitochondrion / RNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / 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 / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / 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
Polyribonucleotide nucleotidyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsYuan, H.S. / Golzarroshan, B.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities.
Authors: Golzarroshan, B. / Lin, C.L. / Li, C.L. / Yang, W.Z. / Chu, L.Y. / Agrawal, S. / Yuan, H.S.
History
DepositionMar 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)141,4252
Polymers141,4252
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.335, 109.334, 84.501
Angle α, β, γ (deg.)90.00, 117.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase 1, mitochondrial / Polynucleotide phosphorylase / 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: 70712.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPT1, PNPASE / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TCS8, polyribonucleotide nucleotidyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.85 % / Preparation: 2011-06-07
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate buffer (pH 5.0), 10% (v/v) 2-propanol, 26% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.796→42.157 Å / Num. obs: 32471 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.03
Reflection shellResolution: 2.796→2.89 Å / Rmerge(I) obs: 0.57 / Num. unique obs: 1594

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U1K

3u1k


Resolution: 2.796→42.157 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1930 6.67 %
Rwork0.1929 --
obs0.1967 28918 88.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.796→42.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 0 66 8555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038618
X-RAY DIFFRACTIONf_angle_d0.5411662
X-RAY DIFFRACTIONf_dihedral_angle_d3.5085294
X-RAY DIFFRACTIONf_chiral_restr0.0431380
X-RAY DIFFRACTIONf_plane_restr0.0031501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7964-2.86640.3933640.2491887X-RAY DIFFRACTION42
2.8664-2.94380.314960.25491256X-RAY DIFFRACTION58
2.9438-3.03050.30731190.251679X-RAY DIFFRACTION78
3.0305-3.12820.33461480.24441938X-RAY DIFFRACTION90
3.1282-3.240.31761400.24212011X-RAY DIFFRACTION94
3.24-3.36970.2771450.21712056X-RAY DIFFRACTION94
3.3697-3.5230.28571520.20472081X-RAY DIFFRACTION96
3.523-3.70860.25941480.18832113X-RAY DIFFRACTION98
3.7086-3.94080.24521710.18472113X-RAY DIFFRACTION98
3.9408-4.24480.20641430.17152145X-RAY DIFFRACTION99
4.2448-4.67150.19231490.15722156X-RAY DIFFRACTION99
4.6715-5.34630.20621540.1622154X-RAY DIFFRACTION99
5.3463-6.73130.26051520.20492175X-RAY DIFFRACTION99
6.7313-42.16170.20631490.16952224X-RAY DIFFRACTION99

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