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- PDB-2a1s: Crystal structure of native PARN nuclease domain -

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Basic information

Entry
Database: PDB / ID: 2a1s
TitleCrystal structure of native PARN nuclease domain
ComponentsPoly(A)-specific ribonuclease PARN
KeywordsHYDROLASE / PARN / DEDD / nuclease domain / R3H
Function / homology
Function and homology information


lncRNA processing / priRNA 3'-end processing / siRNA 3'-end processing / cation binding / RNA modification / box H/ACA sno(s)RNA 3'-end processing / telomerase RNA stabilization / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / miRNA catabolic process ...lncRNA processing / priRNA 3'-end processing / siRNA 3'-end processing / cation binding / RNA modification / box H/ACA sno(s)RNA 3'-end processing / telomerase RNA stabilization / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / miRNA catabolic process / regulation of telomerase RNA localization to Cajal body / female gamete generation / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / ATF4 activates genes in response to endoplasmic reticulum stress / nuclease activity / Deadenylation of mRNA / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of telomere maintenance via telomerase / mRNA 3'-UTR binding / 3'-5'-RNA exonuclease activity / nuclear speck / protein kinase binding / nucleolus / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
R3H-like domain / Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / : / Ribonuclease CAF1 / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. ...R3H-like domain / Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / : / Ribonuclease CAF1 / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / Ribonuclease H-like superfamily/Ribonuclease H / RNA-binding domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWu, M. / Song, H.
CitationJournal: Embo J. / Year: 2005
Title: Structural insight into poly(A) binding and catalytic mechanism of human PARN
Authors: Wu, M. / Reuter, M. / Lilie, H. / Liu, Y. / Wahle, E. / Song, H.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(A)-specific ribonuclease PARN
B: Poly(A)-specific ribonuclease PARN
C: Poly(A)-specific ribonuclease PARN
D: Poly(A)-specific ribonuclease PARN


Theoretical massNumber of molelcules
Total (without water)198,4694
Polymers198,4694
Non-polymers00
Water4,306239
1
A: Poly(A)-specific ribonuclease PARN
D: Poly(A)-specific ribonuclease PARN


Theoretical massNumber of molelcules
Total (without water)99,2342
Polymers99,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-9 kcal/mol
Surface area41010 Å2
MethodPISA
2
B: Poly(A)-specific ribonuclease PARN
C: Poly(A)-specific ribonuclease PARN


Theoretical massNumber of molelcules
Total (without water)99,2342
Polymers99,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-10 kcal/mol
Surface area40790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.540, 123.016, 82.844
Angle α, β, γ (deg.)90.00, 112.59, 90.00
Int Tables number5
Space group name H-MC121
Detailshomodimer is the functional unit

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Components

#1: Protein
Poly(A)-specific ribonuclease PARN / Polyadenylate-specific ribonuclease / Deadenylating nuclease / Deadenylation nuclease / PARN / ...Polyadenylate-specific ribonuclease / Deadenylating nuclease / Deadenylation nuclease / PARN / poly(A) specific nuclease


Mass: 49617.137 Da / Num. of mol.: 4 / Fragment: PARN(1-430)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL_21 star / References: UniProt: O95453, poly(A)-specific ribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, 0.2M ammonium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2004
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 58187 / Num. obs: 58173 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 69.76 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2 / Num. unique all: 5683 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A1R

2a1r


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.89 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 1.12 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25362 1780 3.1 %RANDOM
Rwork0.21864 ---
all0.243 58173 --
obs0.21971 56251 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.465 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å22.19 Å2
2--2.09 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12876 0 0 239 13115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213253
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211733
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.95817829
X-RAY DIFFRACTIONr_angle_other_deg0.815327556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13251558
X-RAY DIFFRACTIONr_chiral_restr0.0780.21898
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214488
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022724
X-RAY DIFFRACTIONr_nbd_refined0.2120.23065
X-RAY DIFFRACTIONr_nbd_other0.2280.213777
X-RAY DIFFRACTIONr_nbtor_other0.0880.27868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2322
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.29
X-RAY DIFFRACTIONr_mcbond_it0.7961.57891
X-RAY DIFFRACTIONr_mcangle_it1.51212796
X-RAY DIFFRACTIONr_scbond_it1.4835362
X-RAY DIFFRACTIONr_scangle_it2.6134.55033
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 121
Rwork0.308 4071
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8477-0.3744-0.4520.06180.17870.17790.1509-0.14940.1768-0.034-0.0575-0.0526-0.10360.0398-0.09340.0609-0.0520.00310.0809-0.0170.093177.4462.119621.2304
21.04530.0575-0.25530.09150.10560.05950.0894-0.14220.0096-0.0485-0.02630.0067-0.00680.0048-0.06310.1150.0205-0.01710.07830.01080.005160.871463.251361.174
30.9106-0.0223-0.16680.02910.07860.0098-0.01180.0992-0.1371-0.0136-0.02260.0074-0.0205-0.02120.03440.07830.02340.00030.1-0.02460.038554.72936.031535.9193
40.9196-0.0214-0.24210.06510.16610.10120.05830.0971-0.06570.029-0.0145-0.0303-0.0065-0.0605-0.04380.0653-0.0218-0.05510.04020.02430.085567.8042-24.4043-3.6458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 361 - 36
2X-RAY DIFFRACTION1AA46 - 14446 - 144
3X-RAY DIFFRACTION1AA170 - 369170 - 369
4X-RAY DIFFRACTION1AA375 - 430375 - 430
6X-RAY DIFFRACTION2BB1 - 391 - 39
7X-RAY DIFFRACTION2BB47 - 14747 - 147
8X-RAY DIFFRACTION2BB173 - 369173 - 369
9X-RAY DIFFRACTION2BB375 - 427375 - 427
11X-RAY DIFFRACTION3CC1 - 361 - 36
12X-RAY DIFFRACTION3CC47 - 14747 - 147
13X-RAY DIFFRACTION3CC170 - 369170 - 369
14X-RAY DIFFRACTION3CC375 - 430375 - 430
16X-RAY DIFFRACTION4DD1 - 381 - 38
17X-RAY DIFFRACTION4DD46 - 14346 - 143
18X-RAY DIFFRACTION4DD170 - 369170 - 369
19X-RAY DIFFRACTION4DD375 - 430375 - 430

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