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- PDB-3d45: Crystal structure of mouse PARN in complex with m7GpppG -

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Basic information

Entry
Database: PDB / ID: 3d45
TitleCrystal structure of mouse PARN in complex with m7GpppG
ComponentsPoly(A)-specific ribonuclease PARN
KeywordsHYDROLASE / PARN / cap analogue / Exonuclease / Magnesium / Metal-binding / Nonsense-mediated mRNA decay / Nuclease / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / : / box H/ACA sno(s)RNA 3'-end processing / Deadenylation of mRNA / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / regulation of telomerase RNA localization to Cajal body ...KSRP (KHSRP) binds and destabilizes mRNA / : / box H/ACA sno(s)RNA 3'-end processing / Deadenylation of mRNA / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / regulation of telomerase RNA localization to Cajal body / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of telomere maintenance via telomerase / postsynapse / nuclear speck / glutamatergic synapse / nucleolus / protein kinase binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. / Ribonuclease H-like superfamily/Ribonuclease H ...Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / 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
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWu, M. / Song, H.
CitationJournal: Structure / Year: 2009
Title: Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.
Authors: Wu, M. / Nilsson, P. / Henriksson, N. / Niedzwiecka, A. / Lim, M.K. / Cheng, Z. / Kokkoris, K. / Virtanen, A. / Song, H.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
B: Poly(A)-specific ribonuclease PARN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3656
Polymers116,7202
Non-polymers1,6454
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area36640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.013, 128.350, 176.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA1 - 343 - 36
21METMETILEILEBB1 - 343 - 36
32PROPROARGARGAA50 - 14052 - 142
42PROPROARGARGBB50 - 14052 - 142
53GLUGLUPROPROAA255 - 350257 - 352
63GLUGLUPROPROBB255 - 350257 - 352
74ALAALAPROPROAA372 - 410374 - 412
84ALAALAPROPROBB372 - 410374 - 412

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Components

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


Mass: 58360.035 Da / Num. of mol.: 2 / Fragment: mPARN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Parn / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21 / References: UniProt: Q8VDG3, poly(A)-specific ribonuclease
#2: Chemical ChemComp-7MG / 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 379.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O8P
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6~10% PEG6000, 100mM MES, pH6.0, 10mM betaine , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→103.69 Å / Num. all: 29592 / Num. obs: 29592 / % possible obs: 96 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.101
Reflection shellResolution: 3→3.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.3 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A1R 1WHV

2a1r

1whv


Resolution: 3→103.69 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.838 / SU B: 40.73 / SU ML: 0.438 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33371 1293 5 %RANDOM
Rwork0.2986 ---
obs0.30035 24512 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.434 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å20 Å20 Å2
2---2.58 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 3→103.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 104 78 6307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226396
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9728661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.07424.603315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.156151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6841523
X-RAY DIFFRACTIONr_chiral_restr0.1030.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024872
X-RAY DIFFRACTIONr_nbd_refined0.2560.23354
X-RAY DIFFRACTIONr_nbtor_refined0.3230.24365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.23
X-RAY DIFFRACTIONr_mcbond_it0.6491.53858
X-RAY DIFFRACTIONr_mcangle_it1.18326116
X-RAY DIFFRACTIONr_scbond_it1.12932886
X-RAY DIFFRACTIONr_scangle_it1.8264.52545
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
988tight positional0.080.05
1004medium positional0.40.5
988tight thermal2.10.5
1004medium thermal1.952
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 84 -
Rwork0.353 1776 -
obs--93.94 %
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)
11.13090.07350.9991.22570.12951.6689-0.0992-0.0627-0.03750.0331-0.0319-0.0387-0.15460.04230.13110.05540.00280.0041-0.19330.0705-0.24025.476519.965814.2994
20.81250.1551-0.46341.398-0.01041.0364-0.0106-0.0134-0.2559-0.02340.05350.1690.22060.0345-0.0429-0.0201-0.00640.0614-0.17750.0397-0.0414-11.0497-13.4144-6.2496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 343 - 36
2X-RAY DIFFRACTION1AA50 - 14052 - 142
3X-RAY DIFFRACTION1AA255 - 350257 - 352
4X-RAY DIFFRACTION1AA372 - 410374 - 412
5X-RAY DIFFRACTION1AA440 - 500442 - 502
6X-RAY DIFFRACTION2BB1 - 343 - 36
7X-RAY DIFFRACTION2BB50 - 14052 - 142
8X-RAY DIFFRACTION2BB255 - 350257 - 352
9X-RAY DIFFRACTION2BB372 - 410374 - 412
10X-RAY DIFFRACTION2BB440 - 500442 - 502

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