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- PDB-3ctr: Crystal structure of the RRM-domain of the poly(A)-specific ribon... -

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Basic information

Entry
Database: PDB / ID: 3ctr
TitleCrystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP
ComponentsPoly(A)-specific ribonuclease PARN
KeywordsHYDROLASE / PARN / Protein-RNA-complex / m7G-cap / m7GTP / RNA recognition motif / RRM / Exonuclease / Magnesium / Metal-binding / Nonsense-mediated mRNA decay / Nuclease / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


: / box H/ACA sno(s)RNA 3'-end processing / RNA modification / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / female gamete generation / regulation of telomerase RNA localization to Cajal body ...: / box H/ACA sno(s)RNA 3'-end processing / RNA modification / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / female gamete generation / regulation of telomerase RNA localization to Cajal body / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / ATF4 activates genes in response to endoplasmic reticulum stress / Deadenylation of mRNA / nuclease activity / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / mRNA 3'-UTR binding / postsynapse / nuclear speck / glutamatergic synapse / nucleolus / protein kinase binding / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
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. / RRM (RNA recognition motif) domain / 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. / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsMonecke, T. / Schell, S. / Dickmanns, A. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode.
Authors: Monecke, T. / Schell, S. / Dickmanns, A. / Ficner, R.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2013Group: Data collection
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Poly(A)-specific ribonuclease PARN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3602
Polymers11,8221
Non-polymers5381
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Poly(A)-specific ribonuclease PARN
hetero molecules

A: Poly(A)-specific ribonuclease PARN
hetero molecules

A: Poly(A)-specific ribonuclease PARN
hetero molecules

A: Poly(A)-specific ribonuclease PARN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4428
Polymers47,2894
Non-polymers2,1534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area9560 Å2
ΔGint-53.8 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.107, 81.107, 78.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

DetailsThe asymmentric unit contains one monomer representing the functional m7G-cap binding motif (RRM) of PARN

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Components

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


Mass: 11822.170 Da / Num. of mol.: 1 / Fragment: RNA-recognition-motif of PARN (residues 445-540)
Source method: isolated from a genetically manipulated source
Details: This vector additionally introduces the amino acid sequence gplgs before the N-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: PARN, DAN / Plasmid: pGEX-6P-PARN3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE3) / References: UniProt: O95453, poly(A)-specific ribonuclease
#2: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2 M LiSO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A11.078
SYNCHROTRONBESSY 14.220.9778, 0.97861, 0.91841
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDMar 28, 2007mirrors
MAR CCD 165 mm2CCDApr 18, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed exit double crystal Si-111, horizontally focussingSINGLE WAVELENGTHMx-ray1
2Double Crystal Monochromator Si-111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0781
20.97781
30.978611
40.918411
ReflectionResolution: 2.1→30 Å / Num. all: 7925 / Num. obs: 7918 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 13.6 % / Rsym value: 0.038 / Net I/σ(I): 67.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 14.4 / Num. unique all: 776 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.168 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24287 382 4.9 %RANDOM
Rwork0.20959 ---
all0.21124 7466 --
obs0.21124 7448 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.363 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2---1.83 Å20 Å2
3---3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms602 0 33 69 704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022654
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.998898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.203574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.77724.82829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8231598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.778151
X-RAY DIFFRACTIONr_chiral_restr0.0970.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02486
X-RAY DIFFRACTIONr_nbd_refined0.1950.2279
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.28
X-RAY DIFFRACTIONr_mcbond_it0.8761.5384
X-RAY DIFFRACTIONr_mcangle_it1.512604
X-RAY DIFFRACTIONr_scbond_it2.0073336
X-RAY DIFFRACTIONr_scangle_it3.2074.5294
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 26 -
Rwork0.249 509 -
obs-509 99.81 %

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