[English] 日本語
Yorodumi
- PDB-5o1y: Structure of Nrd1 RNA binding domain in complex with RNA (GUAA) -

+
Open data


ID or keywords:

Loading...

-
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 / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / CUT catabolic process / 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 / snRNA 3'-end processing / CUT catabolic process / 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)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more