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- PDB-2xnr: Structural insights into cis element recognition of non- polyaden... -

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Basic information

Entry
Database: PDB / ID: 2xnr
TitleStructural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM
Components
  • 5'-R(*UP*UP*CP*UP*UP*AP*UP*UP*CP*UP*UP*A)-3'
  • NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / TRANSCRIPTION TERMINATION / RNA RECOGNITION / RRM / RNA PROCESSING
Function / homology
Function and homology information


transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing / snRNA 3'-end processing / CUT catabolic process / tRNA 3'-end processing / nuclear mRNA surveillance / SUMOylation of RNA binding proteins ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / termination of RNA polymerase II transcription, exosome-dependent / sno(s)RNA 3'-end processing / snRNA 3'-end processing / CUT catabolic process / tRNA 3'-end processing / nuclear mRNA surveillance / SUMOylation of RNA binding proteins / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nab3, RNA recognition motif / : / Anticodon-binding domain superfamily / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...Nab3, RNA recognition motif / : / Anticodon-binding domain superfamily / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / RNA / RNA (> 10) / Nuclear polyadenylated RNA-binding protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLunde, B.M. / Horner, M. / Meinhart, A.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural Insights Into Cis Element Recognition of Non-Polyadenylated Rnas by the Nab3-Rrm.
Authors: Lunde, B.M. / Horner, M. / Meinhart, A.
History
DepositionAug 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3
C: 5'-R(*UP*UP*CP*UP*UP*AP*UP*UP*CP*UP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8264
Polymers14,7082
Non-polymers1182
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-3.5 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.640, 30.640, 82.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3


Mass: 11034.574 Da / Num. of mol.: 1 / Fragment: RNA RECOGNITION MOTIF, RESIDUES 329-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P38996
#2: RNA chain 5'-R(*UP*UP*CP*UP*UP*AP*UP*UP*CP*UP*UP*A)-3'


Mass: 3673.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF NAB3-RRM DOMAIN WITH N-TERMINAL HIS-TAG AND THROMBIN CLEAVAGE SITE

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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: 2.15 Å3/Da / Density % sol: 48.94 % / Description: NONE
Crystal growpH: 4.5
Details: 85MM SODIUM ACETATE BUFFER PH 4.6, 170MM AMMONIUM ACETATE, 25.5% (W/V) PEG 4000, 15% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978243
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978243 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 9510 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.91
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.26 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XNQ

2xnq


Resolution: 1.6→30.64 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.294 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 501 5 %RANDOM
Rwork0.16032 ---
obs0.1615 9510 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 65 8 47 724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2522.085938
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85825.16131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19115119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.955153
X-RAY DIFFRACTIONr_chiral_restr0.0840.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021497
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6951.5379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3852607
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1633313
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4344.5331
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 36 -
Rwork0.218 690 -
obs--100 %
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)
10.8918-0.0851-0.15252.9275-0.01042.00920.02630.0007-0.02910.0216-0.0778-0.0372-0.0090.05740.05150.0676-0.00150.00850.0564-0.0030.052110.34717.96075.1212
215.0938-0.6189-7.43587.7742.977928.4041-0.47450.6839-0.8360.17590.2636-0.53541.26720.72030.21090.08550.03340.01440.0838-0.05960.088219.2540.89048.9613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A328 - 402
2X-RAY DIFFRACTION2C0 - 4

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