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- PDB-2a1r: Crystal structure of PARN nuclease domain -

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Basic information

Entry
Database: PDB / ID: 2a1r
TitleCrystal structure of PARN nuclease domain
Components
  • 5'-R(*AP*AP*A)-3'
  • Poly(A)-specific ribonuclease PARN
KeywordsHYDROLASE/RNA / PARN / DEDD / Nuclease domain / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


: / 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 / regulation of telomerase RNA localization to Cajal body / female gamete generation / miRNA catabolic process ...: / 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 / regulation of telomerase RNA localization to Cajal body / female gamete generation / miRNA catabolic process / 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 / postsynapse / nuclear speck / glutamatergic synapse / nucleolus / protein kinase binding / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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. / Ribonuclease H-like superfamily/Ribonuclease H / RNA-binding domain superfamily ...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. / 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
RNA / Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-R(*AP*AP*A)-3'
D: 5'-R(*AP*AP*A)-3'
A: Poly(A)-specific ribonuclease PARN
B: Poly(A)-specific ribonuclease PARN


Theoretical massNumber of molelcules
Total (without water)101,1204
Polymers101,1204
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.778, 92.401, 159.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailshomodimer is the functional unit

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Components

#1: RNA chain 5'-R(*AP*AP*A)-3'


Mass: 942.660 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Poly(A)-specific ribonuclease PARN / Polyadenylate-specific ribonuclease / Deadenylating nuclease / Deadenylation nuclease / PARN


Mass: 49617.137 Da / Num. of mol.: 2 / Fragment: PARN(1-430)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARN / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 star / References: UniProt: O95453, poly(A)-specific ribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.68 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, 0.2M ammonium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2ammonium tartrate11
3H2O11
4PEG 335012
5ammonium tartrate12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791, 0.9793, 0.9762
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2004
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97621
ReflectionResolution: 2.6→50 Å / Num. all: 36514 / Num. obs: 36318 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2353 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.795 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.402 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23561 1610 4.9 %RANDOM
Rwork0.21823 ---
all0.2208 36514 --
obs0.21909 31218 97.24 %-
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: 49.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å20 Å20 Å2
2---5.57 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 126 0 153 5078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225104
X-RAY DIFFRACTIONr_bond_other_d0.0020.024396
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9856902
X-RAY DIFFRACTIONr_angle_other_deg0.794310320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465588
X-RAY DIFFRACTIONr_chiral_restr0.0760.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025526
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021060
X-RAY DIFFRACTIONr_nbd_refined0.2080.21174
X-RAY DIFFRACTIONr_nbd_other0.2320.25126
X-RAY DIFFRACTIONr_nbtor_other0.0870.22760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.25
X-RAY DIFFRACTIONr_mcbond_it1.0541.52987
X-RAY DIFFRACTIONr_mcangle_it1.99724824
X-RAY DIFFRACTIONr_scbond_it1.77232117
X-RAY DIFFRACTIONr_scangle_it3.1444.52078
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 97
Rwork0.306 2079
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)
10.5417-0.0491-0.01091.4404-0.20610.45790.0163-0.03830.1364-0.0615-0.0006-0.13120.01440.0909-0.01570.07130.05520.03330.1014-0.04070.111156.104552.772720.4356
20.6580.5157-0.10813.0675-0.03350.452-0.03090.0519-0.03260.08180.11740.1342-0.0683-0.0957-0.08650.0920.0334-0.00110.08730.01190.042937.272514.312117.7321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 401 - 40
2X-RAY DIFFRACTION1AC46 - 14346 - 143
3X-RAY DIFFRACTION1AC257 - 369257 - 369
4X-RAY DIFFRACTION1AC375 - 423375 - 423
6X-RAY DIFFRACTION1CA501 - 5031 - 3
7X-RAY DIFFRACTION2BD1 - 401 - 40
8X-RAY DIFFRACTION2BD50 - 14350 - 143
9X-RAY DIFFRACTION2BD261 - 369261 - 369
10X-RAY DIFFRACTION2BD375 - 423375 - 423
12X-RAY DIFFRACTION2DB601 - 6031 - 3

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