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- PDB-3u1k: Crystal structure of human PNPase -

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Basic information

Entry
Database: PDB / ID: 3u1k
TitleCrystal structure of human PNPase
ComponentsPolyribonucleotide nucleotidyltransferase 1, mitochondrial
KeywordsTRANSFERASE / RNase PH / KH domain / exoribonuclease
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 catabolic process / mitochondrial RNA 5'-end processing / Mitochondrial RNA degradation / positive regulation of miRNA catabolic process ...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 catabolic process / mitochondrial RNA 5'-end processing / 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 / poly(U) RNA binding / RNA catabolic process / response to growth hormone / miRNA binding / protein homotrimerization / mRNA catabolic process / cellular response to interferon-beta / response to cAMP / mitochondrion organization / liver regeneration / protein homooligomerization / mitochondrial intermembrane space / mRNA processing / 3'-5'-RNA exonuclease activity / cellular response to oxidative stress / ribosome / regulation of cell cycle / mitochondrial matrix / endoplasmic reticulum membrane / mitochondrion / RNA binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / K Homology domain, type 1 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / K Homology domain, type 1 / 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 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Arc Repressor Mutant, subunit A / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Polyribonucleotide nucleotidyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLin, C.L. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation
Authors: Lin, C.L. / Wang, Y.-T. / Yang, W.-Z. / Hsiao, Y.-Y. / Yuan, H.S.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
C: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
B: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
D: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,77512
Polymers275,2384
Non-polymers1,5378
Water21,1141172
1
A: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
hetero molecules

A: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
hetero molecules

A: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,5829
Polymers206,4293
Non-polymers1,1536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14890 Å2
ΔGint-40 kcal/mol
Surface area70360 Å2
MethodPISA
2
C: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
B: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
D: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,5829
Polymers206,4293
Non-polymers1,1536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-41 kcal/mol
Surface area69910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)289.753, 289.753, 92.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 68809.609 Da / Num. of mol.: 4 / Fragment: UNP residues 46-669
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL
References: UniProt: Q8TCS8, polyribonucleotide nucleotidyltransferase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1172 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVAL 121 IS BASED ON THE NATURAL VALIANT.

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10%(v/v) 2-Propanol, 0.1M Sodium citrate tribasic dihydrate, 26%(v/v) Polyethylene glycol 400 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / 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: 2.13→30 Å / Num. all: 162293 / Num. obs: 162293 / % possible obs: 100 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.39 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.8
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.7 / Num. unique all: 16272 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GCM

3gcm


Resolution: 2.13→28.5 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.839 / SU ML: 0.52 / σ(F): 1.97 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 8129 5.01 %RANDOM
Rwork0.1799 ---
obs0.1821 162282 99.96 %-
all-162282 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.924 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 110.85 Å2 / Biso mean: 42.4901 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.1554 Å2-0 Å20 Å2
2---3.1554 Å20 Å2
3---7.3758 Å2
Refinement stepCycle: LAST / Resolution: 2.13→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18929 0 104 1172 20205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719327
X-RAY DIFFRACTIONf_angle_d1.07126174
X-RAY DIFFRACTIONf_chiral_restr0.0793063
X-RAY DIFFRACTIONf_plane_restr0.0043390
X-RAY DIFFRACTIONf_dihedral_angle_d15.7817262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1303-2.15450.31562780.225651445422100
2.1545-2.17990.28642730.217151765449100
2.1799-2.20640.28362880.207950985386100
2.2064-2.23430.25442770.204851115388100
2.2343-2.26370.27932730.202751945467100
2.2637-2.29470.25942720.205450595331100
2.2947-2.32750.27483000.202251255425100
2.3275-2.36220.25122530.195451475400100
2.3622-2.39910.25713220.193351145436100
2.3991-2.43840.28952680.199851235391100
2.4384-2.48050.27932720.200751355407100
2.4805-2.52550.28222560.207351555411100
2.5255-2.57410.26372670.193151825449100
2.5741-2.62660.27012410.189151565397100
2.6266-2.68370.26562670.196451105377100
2.6837-2.7460.26442520.203452055457100
2.746-2.81460.25872530.202551475400100
2.8146-2.89070.25712770.205451395416100
2.8907-2.97560.27452630.212151195382100
2.9756-3.07160.24032710.205551455416100
3.0716-3.18120.26752850.204851155400100
3.1812-3.30840.22722940.196351335427100
3.3084-3.45870.22052650.187251345399100
3.4587-3.64070.23832470.176951745421100
3.6407-3.86830.20012640.169251725436100
3.8683-4.16610.19332750.154451015376100
4.1661-4.58380.16922820.139551285410100
4.5838-5.24350.16752700.141251405410100
5.2435-6.59250.19152620.172751655427100
6.5925-28.36850.16682620.15975107536999

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