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- PDB-5o1y: Structure of Nrd1 RNA binding domain in complex with RNA (GUAA) -

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Basic information

Entry
Database: PDB / ID: 5o1y
TitleStructure of Nrd1 RNA binding domain in complex with RNA (GUAA)
Components
  • Protein NRD1
  • RNA (5'-R(*GP*UP*AP*A)-3')
KeywordsTRANSCRIPTION / Nrd1 / Nrd1 complex / RRM / RNA-binding / non-coding transcription
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 / tRNA 3'-end processing / CUT catabolic process / snRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing ...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 / tRNA 3'-end processing / CUT catabolic process / snRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing / protein domain specific binding / mRNA binding / RNA binding / nucleus
Similarity search - Function
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / 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
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsFranco-Echevarria, E. / Perez-Canadillas, J.M. / Gonzalez, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
CSIC Spain
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition.
Authors: Franco-Echevarria, E. / Gonzalez-Polo, N. / Zorrilla, S. / Martinez-Lumbreras, S. / Santiveri, C.M. / Campos-Olivas, R. / Sanchez, M. / Calvo, O. / Gonzalez, B. / Perez-Canadillas, J.M.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NRD1
B: RNA (5'-R(*GP*UP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6205
Polymers21,3732
Non-polymers2463
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint2 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.936, 64.936, 158.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein NRD1


Mass: 20108.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NRD1, YNL251C, N0868 / Production host: Escherichia coli (E. coli) / References: UniProt: P53617
#2: RNA chain RNA (5'-R(*GP*UP*AP*A)-3')


Mass: 1264.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1M Sodium Potassium Phosphate pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.45→60.08 Å / Num. obs: 12717 / % possible obs: 96.1 % / Redundancy: 16.7 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.1 / Net I/σ(I): 28.2
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.97 / Rpim(I) all: 0.154

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O1W

5o1w


Resolution: 2.45→60.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.754 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21724 621 4.9 %RANDOM
Rwork0.19668 ---
obs0.1977 12040 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.307 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2--2.05 Å20 Å2
3----4.11 Å2
Refinement stepCycle: 1 / Resolution: 2.45→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 84 16 38 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191458
X-RAY DIFFRACTIONr_bond_other_d0.0020.021268
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.8942000
X-RAY DIFFRACTIONr_angle_other_deg0.97432952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30223.78866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41815212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.254158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
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_it3.415.824652
X-RAY DIFFRACTIONr_mcbond_other3.4095.806650
X-RAY DIFFRACTIONr_mcangle_it5.5498.7812
X-RAY DIFFRACTIONr_mcangle_other5.5468.711813
X-RAY DIFFRACTIONr_scbond_it3.9166.637806
X-RAY DIFFRACTIONr_scbond_other3.9146.637806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5229.7881189
X-RAY DIFFRACTIONr_long_range_B_refined9.26567.6561601
X-RAY DIFFRACTIONr_long_range_B_other9.26867.7131600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 42 -
Rwork0.337 909 -
obs--100 %

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