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- PDB-5o1x: Structure of Nrd1 RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 5o1x
TitleStructure of Nrd1 RNA binding domain
ComponentsProtein NRD1
KeywordsTRANSCRIPTION / Nrd1 / RRM / RNA-binding / transcription non-coding RNAs / Nrd1 complex
Function / homology
Function and homology information


transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / CUT catabolic process / snRNA 3'-end processing / tRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / CUT catabolic process / snRNA 3'-end processing / tRNA 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
THIOCYANATE ION / Protein NRD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFranco-Echevarria, E. / Perez-Canadillas, J.M. / Gonzalez, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
CSICBFU2014-53762-P, CTQ2014-52633 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

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Assembly

Deposited unit
A: Protein NRD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,00816
Polymers20,1091
Non-polymers89915
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-7 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 58.390, 92.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Protein NRD1


Mass: 20108.586 Da / Num. of mol.: 1 / Fragment: UNP residues 290-468
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M Potassium Thiocyanate, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2015 / Details: KB focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→92.45 Å / Num. obs: 23596 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.018 / Net I/σ(I): 26.82
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 6.1 / Num. measured obs: 24279 / Num. unique all: 1197 / CC1/2: 0.95 / Rpim(I) all: 0.136 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O1W

5o1w


Resolution: 1.6→50.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.684 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20805 1141 4.8 %RANDOM
Rwork0.17758 ---
obs0.17904 22455 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.902 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.6→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 52 138 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191485
X-RAY DIFFRACTIONr_bond_other_d0.0020.021378
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9482009
X-RAY DIFFRACTIONr_angle_other_deg0.89133184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34123.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75315232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.277159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211698
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
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_it1.0731.935707
X-RAY DIFFRACTIONr_mcbond_other1.0581.924698
X-RAY DIFFRACTIONr_mcangle_it1.8792.883888
X-RAY DIFFRACTIONr_mcangle_other1.882.887889
X-RAY DIFFRACTIONr_scbond_it1.1682.11778
X-RAY DIFFRACTIONr_scbond_other1.1572.105770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9663.0771110
X-RAY DIFFRACTIONr_long_range_B_refined4.68816.5731706
X-RAY DIFFRACTIONr_long_range_B_other4.38716.0381644
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
Rfree0.293 91 -
Rwork0.234 1663 -
obs--100 %

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