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- PDB-5o1w: Structure of Nrd1 RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 5o1w
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 / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance ...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 / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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

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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)21,3582
Polymers21,2961
Non-polymers621
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.991, 60.991, 157.958
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: 21295.924 Da / Num. of mol.: 1 / Fragment: UNP residues 301-489
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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 12% PEG 8000, 0.1 M Bicine pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→48.14 Å / Num. all: 13708 / Num. obs: 383024 / % possible obs: 99.1 % / Redundancy: 24.5 % / Net I/σ(I): 32.1
Reflection shellRedundancy: 26.8 % / Num. measured obs: 34968 / Num. unique all: 1307 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→56.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.104 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23297 698 5 %RANDOM
Rwork0.2068 ---
obs0.20796 13317 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.946 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--2.14 Å20 Å2
3----4.28 Å2
Refinement stepCycle: 1 / Resolution: 2.3→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 4 42 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191369
X-RAY DIFFRACTIONr_bond_other_d0.0020.021281
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9481862
X-RAY DIFFRACTIONr_angle_other_deg0.90632954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78623.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.598158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
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_it1.7614.203667
X-RAY DIFFRACTIONr_mcbond_other1.7614.197666
X-RAY DIFFRACTIONr_mcangle_it2.9096.294832
X-RAY DIFFRACTIONr_mcangle_other2.9086.302833
X-RAY DIFFRACTIONr_scbond_it2.1444.433701
X-RAY DIFFRACTIONr_scbond_other2.1324.434701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5736.5181031
X-RAY DIFFRACTIONr_long_range_B_refined7.90639.2555556
X-RAY DIFFRACTIONr_long_range_B_other7.90639.2625557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 55 -
Rwork0.314 964 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 8.3334 Å / Origin y: 21.8696 Å / Origin z: 19.1437 Å
111213212223313233
T0.025 Å20.0015 Å20.0177 Å2-0.0628 Å20.0524 Å2--0.0713 Å2
L3.3729 °21.0971 °2-2.7855 °2-1.6388 °2-2.136 °2--5.8192 °2
S-0.1208 Å °-0.0641 Å °0.0794 Å °0.0297 Å °0.1744 Å °0.2653 Å °0.1003 Å °0.0489 Å °-0.0536 Å °

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