[English] 日本語
Yorodumi
- PDB-6qit: Crystal structure of CAG repeats with synthetic CMBL3b compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qit
TitleCrystal structure of CAG repeats with synthetic CMBL3b compound
ComponentsRNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
KeywordsRNA / CAG repeats / CMBL / RNA complex with ligand
Function / homologyCMBL3a / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.501 Å
AuthorsKiliszek, A. / Blaszczyk, L. / Rypniewski, W. / Nakatani, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
NCN 2017/26/E/NZ1/00950 Poland
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Authors: Mukherjee, S. / Blaszczyk, L. / Rypniewski, W. / Falschlunger, C. / Micura, R. / Murata, A. / Dohno, C. / Nakatani, K. / Kiliszek, A.
History
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2618
Polymers10,2584
Non-polymers2,0024
Water3,153175
1
A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
B: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1304
Polymers5,1292
Non-polymers1,0012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
D: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1304
Polymers5,1292
Non-polymers1,0012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.233, 50.989, 39.554
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 2564.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-J48 / CMBL3a


Mass: 500.529 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H26N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20 mM magnesium acetate and 1.7 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→29.3 Å / Num. obs: 20979 / % possible obs: 96.1 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3317 / CC1/2: 0.65 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.501→29.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1049 5.01 %
Rwork0.1504 --
obs0.1527 20920 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 680 148 175 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009957
X-RAY DIFFRACTIONf_angle_d1.4841453
X-RAY DIFFRACTIONf_dihedral_angle_d11.336582
X-RAY DIFFRACTIONf_chiral_restr0.069164
X-RAY DIFFRACTIONf_plane_restr0.01186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5013-1.58040.28551460.21622764X-RAY DIFFRACTION94
1.5804-1.67940.2481490.16932820X-RAY DIFFRACTION96
1.6794-1.80910.22021500.15552841X-RAY DIFFRACTION96
1.8091-1.99110.23561490.1422833X-RAY DIFFRACTION97
1.9911-2.27910.18151510.1522872X-RAY DIFFRACTION97
2.2791-2.87110.23651530.17752893X-RAY DIFFRACTION97
2.8711-29.30570.15531510.13042848X-RAY DIFFRACTION95

+
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://pdbjlvh1.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