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- PDB-5o1z: Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) -

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Basic information

Entry
Database: PDB / ID: 5o1z
TitleStructure of Nrd1 RNA binding domain in complex with RNA (CGUAAA)
Components
  • Protein NRD1
  • RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
B: RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)22,0082
Polymers22,0082
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.529, 64.529, 157.033
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 / 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: RNA chain RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')


Mass: 1899.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 66.88 %
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: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.4→59.69 Å / Num. obs: 5025 / % possible obs: 100 % / Redundancy: 23.9 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Net I/σ(I): 22.2
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 8.5 / Num. unique all: 989 / Rpim(I) all: 0.116 / % possible all: 100

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Processing

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

5o1w


Resolution: 3.4→59.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.849 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21585 246 4.9 %RANDOM
Rwork0.18113 ---
obs0.18301 4739 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.054 Å2
Baniso -1Baniso -2Baniso -3
1-6.58 Å20 Å20 Å2
2--6.58 Å20 Å2
3----13.17 Å2
Refinement stepCycle: 1 / Resolution: 3.4→59.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 126 0 1 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0181492
X-RAY DIFFRACTIONr_bond_other_d0.0020.021268
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.8662060
X-RAY DIFFRACTIONr_angle_other_deg0.94432956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92423.78866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.406158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
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_it2.9738.288651
X-RAY DIFFRACTIONr_mcbond_other2.9738.284650
X-RAY DIFFRACTIONr_mcangle_it4.96512.424812
X-RAY DIFFRACTIONr_mcangle_other4.96312.429813
X-RAY DIFFRACTIONr_scbond_it3.5999.464841
X-RAY DIFFRACTIONr_scbond_other3.5979.471842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.02914.1181249
X-RAY DIFFRACTIONr_long_range_B_refined8.08597.9381630
X-RAY DIFFRACTIONr_long_range_B_other8.08397.9431631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 9 -
Rwork0.254 331 -
obs--100 %

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