[English] 日本語
Yorodumi
- PDB-5ca5: Structure of the C. elegans NONO-1 homodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ca5
TitleStructure of the C. elegans NONO-1 homodimer
ComponentsNONO-1
KeywordsRNA BINDING PROTEIN / DBHS homodimer
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / mRNA splicing, via spliceosome / nucleic acid binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription / RNA binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Special / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NONO (Conserved nuclear protein, aka PSF) homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKnott, G.J. / Bond, C.S.
CitationJournal: Protein Sci. / Year: 2015
Title: Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture, and function.
Authors: Knott, G.J. / Lee, M. / Passon, D.M. / Fox, A.H. / Bond, C.S.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: 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: NONO-1
B: NONO-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5966
Polymers59,3482
Non-polymers2484
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-40 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.318, 63.115, 83.838
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsGel Filtration has been used to determine the biological unit content

-
Components

#1: Protein NONO-1


Mass: 29673.836 Da / Num. of mol.: 2 / Fragment: unp residues 95-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nono-1, CELE_F25B5.7, F25B5.7 / Plasmid: pCDF-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): 2DE3 / References: UniProt: B3GWA1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 % / Description: Thick plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.1 M Ammonium sulphate, 15.0 - 20.0 % PEG 3350
Temp details: +/- 1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9658 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9658 Å / Relative weight: 1
ReflectionResolution: 2.4→19.67 Å / Num. obs: 23755 / Biso Wilson estimate: 52.22 Å2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WII

4wii


Resolution: 2.4→19.67 Å / Cor.coef. Fo:Fc: 0.9087 / Cor.coef. Fo:Fc free: 0.8532 / SU R Cruickshank DPI: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.443 / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.3008 1206 5.08 %RANDOM
Rwork0.2429 ---
obs0.246 23755 97.52 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-3.7582 Å20 Å2-1.7043 Å2
2---0.6991 Å20 Å2
3----3.0591 Å2
Refine analyzeLuzzati coordinate error obs: 0.458 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 16 148 4176
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1513SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes599HARMONIC5
X-RAY DIFFRACTIONt_it4107HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion21.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion501SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4533SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.285 108 4.03 %
Rwork0.216 2573 -
all0.2187 2681 -
obs--97.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0577-0.2149-0.18671.0610.25621.19750.0023-0.02480.03880.15690.133-0.0559-0.01380.0302-0.13520.02410.00240.0081-0.5154-0.0077-0.463720.249-5.109618.4571
20.0663-0.1297-0.26420.83980.12940.9641-0.02670.04020.00870.00810.1216-0.0593-0.0196-0.0049-0.0949-0.0439-0.00260.0055-0.4932-0.0123-0.453520.10196.610120.4311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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