[English] 日本語
Yorodumi
- PDB-4yn6: Structural Insight reveals dynamics in repeating r(CAG) transcrip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yn6
TitleStructural Insight reveals dynamics in repeating r(CAG) transcript found in Huntington's disease (HD) and Spinocerebellar ataxias (SCAs)
ComponentsRNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
KeywordsRNA / Trinucleotide repeat / Huntington's disease (HD) / Spinocerebellar ataxias (SCAs)
Function / homologyPHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.301 Å
AuthorsTawani, A. / Kumar, A.
CitationJournal: Plos One / Year: 2015
Title: Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs)
Authors: Tawani, A. / Kumar, A.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 2, 2015Group: Data collection
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4074
Polymers12,2172
Non-polymers1902
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-17 kcal/mol
Surface area6700 Å2
Unit cell
Length a, b, c (Å)46.074, 46.074, 133.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

PO4

21B-101-

PO4

31A-212-

HOH

41A-214-

HOH

51A-221-

HOH

61B-211-

HOH

71B-217-

HOH

-
Components

#1: RNA chain RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*AP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*C)-3')


Mass: 6108.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50mM Tris HCl, 25mM Magnesium Sulphate and 1.8M Ammonium Sulfate
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 7642 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 7 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootphasing
RefinementResolution: 2.301→44.401 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 210 4.51 %RANDOM
Rwork0.2168 ---
obs0.2189 4657 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→44.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 814 10 54 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005916
X-RAY DIFFRACTIONf_angle_d1.3871424
X-RAY DIFFRACTIONf_dihedral_angle_d15.266450
X-RAY DIFFRACTIONf_chiral_restr0.159190
X-RAY DIFFRACTIONf_plane_restr0.00638
LS refinement shellResolution: 1.95→2.3006 Å
RfactorNum. reflection% reflection
Rfree0.2607 210 -
Rwork0.2168 4447 -
obs--99 %

+
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