[English] 日本語
Yorodumi
- PDB-6ynk: Crystal structure of YTHDC1 with compound DHU_DC1_068 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ynk
TitleCrystal structure of YTHDC1 with compound DHU_DC1_068
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-P0K / DI(HYDROXYETHYL)ETHER / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBedi, R.K. / Huang, D. / Wiedmer, L. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: Eur J Med Chem Rep / Year: 2022
Title: Structure-based design of ligands of the m6A-RNA reader YTHDC1
Authors: Li, Y. / Bedi, R.K. / Nai, F. / von Roten, V. / Dolbois, A. / Zalesak, F. / Nachawati, R. / Huang, D. / Caflisch, A.
History
DepositionApr 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YTHDC1
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,27913
Polymers41,9342
Non-polymers1,34511
Water10,395577
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4915
Polymers20,9671
Non-polymers5234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7898
Polymers20,9671
Non-polymers8227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.620, 103.630, 41.960
Angle α, β, γ (deg.)90.000, 104.708, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein YTHDC1


Mass: 20967.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-P0K / 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione


Mass: 235.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40.6 Å / Num. obs: 78966 / % possible obs: 98.4 % / Redundancy: 2.69 % / Biso Wilson estimate: 12.54 Å2 / CC1/2: 1 / Net I/σ(I): 22.27
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 12558 / CC1/2: 0.924

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.3→40.59 Å / SU ML: 0.1176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4534
RfactorNum. reflection% reflection
Rfree0.2021 3946 5 %
Rwork0.1781 --
obs0.1793 78870 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.87 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 81 577 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472740
X-RAY DIFFRACTIONf_angle_d0.77823726
X-RAY DIFFRACTIONf_chiral_restr0.0762402
X-RAY DIFFRACTIONf_plane_restr0.0052463
X-RAY DIFFRACTIONf_dihedral_angle_d24.1143373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.25481310.24262484X-RAY DIFFRACTION90.05
1.32-1.330.25491380.2272629X-RAY DIFFRACTION97.95
1.33-1.350.25941420.23172698X-RAY DIFFRACTION98.75
1.35-1.370.24641410.23282684X-RAY DIFFRACTION99.16
1.37-1.390.24551430.21932702X-RAY DIFFRACTION99.65
1.39-1.410.22921410.20912678X-RAY DIFFRACTION99.44
1.41-1.430.22941420.21622702X-RAY DIFFRACTION99.61
1.43-1.450.21561420.20592695X-RAY DIFFRACTION99.54
1.45-1.480.25261420.20462702X-RAY DIFFRACTION99.61
1.48-1.510.21841420.19332690X-RAY DIFFRACTION99.09
1.51-1.540.24061410.18772676X-RAY DIFFRACTION99.05
1.54-1.570.22321410.18652693X-RAY DIFFRACTION98.54
1.57-1.60.24481410.18752664X-RAY DIFFRACTION99.33
1.6-1.640.20911410.19252696X-RAY DIFFRACTION99.37
1.64-1.680.21221420.17152682X-RAY DIFFRACTION98.84
1.68-1.720.19671430.18122720X-RAY DIFFRACTION99.38
1.72-1.780.19161410.18852679X-RAY DIFFRACTION99.51
1.78-1.830.23921430.18662710X-RAY DIFFRACTION99.37
1.83-1.90.18491420.1782696X-RAY DIFFRACTION98.99
1.9-1.970.21521410.17682686X-RAY DIFFRACTION99.02
1.97-2.060.19491400.17082662X-RAY DIFFRACTION98.42
2.06-2.170.17631410.16452666X-RAY DIFFRACTION97.84
2.17-2.310.19641420.17452700X-RAY DIFFRACTION98.68
2.31-2.490.22851400.17782657X-RAY DIFFRACTION97.66
2.49-2.740.18621400.18572663X-RAY DIFFRACTION98.77
2.74-3.130.20031420.1792705X-RAY DIFFRACTION98.65
3.13-3.950.181400.15352645X-RAY DIFFRACTION96.3
3.95-40.590.17751410.15972660X-RAY DIFFRACTION96.16

+
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