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- PDB-6ynj: Crystal structure of YTHDC1 with compound DHU_DC1_046 -

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Basic information

Entry
Database: PDB / ID: 6ynj
TitleCrystal structure of YTHDC1 with compound DHU_DC1_046
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / 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 / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / 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-P0N / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTHDC1
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,38013
Polymers41,9342
Non-polymers1,44611
Water9,818545
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7076
Polymers20,9671
Non-polymers7405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6737
Polymers20,9671
Non-polymers7066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.830, 103.990, 42.360
Angle α, β, γ (deg.)90.000, 105.534, 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

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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-P0N / (2~{R})-2-(2-chlorophenyl)-5,5-dimethyl-morpholine


Mass: 225.715 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16ClNO / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5

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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: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.82 Å / Num. obs: 52407 / % possible obs: 97.9 % / Redundancy: 3.26 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.41
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8394 / CC1/2: 0.983

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Processing

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

4r3h


Resolution: 1.5→40.81 Å / SU ML: 0.1415 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.1247
RfactorNum. reflection% reflection
Rfree0.1993 2621 5 %
Rwork0.1696 --
obs0.1711 52370 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 85 545 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522787
X-RAY DIFFRACTIONf_angle_d0.80933798
X-RAY DIFFRACTIONf_chiral_restr0.0827410
X-RAY DIFFRACTIONf_plane_restr0.0047470
X-RAY DIFFRACTIONf_dihedral_angle_d24.4492387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.26531360.22142578X-RAY DIFFRACTION95.23
1.52-1.550.2131350.1962575X-RAY DIFFRACTION98.15
1.55-1.580.21931390.18982629X-RAY DIFFRACTION98.37
1.58-1.620.22911370.18342609X-RAY DIFFRACTION98.35
1.62-1.660.24531410.18122664X-RAY DIFFRACTION98.35
1.66-1.70.20171350.17852581X-RAY DIFFRACTION98.16
1.7-1.740.19721380.18762605X-RAY DIFFRACTION97.75
1.74-1.80.23361360.19172595X-RAY DIFFRACTION98.1
1.8-1.850.23231370.19022602X-RAY DIFFRACTION96.75
1.85-1.920.19691400.17812646X-RAY DIFFRACTION98
1.92-20.21631370.17392610X-RAY DIFFRACTION98.88
2-2.090.20791380.17092619X-RAY DIFFRACTION98.53
2.09-2.20.1891390.16882639X-RAY DIFFRACTION98.86
2.2-2.330.20271380.16722631X-RAY DIFFRACTION98.19
2.33-2.510.20331390.17472627X-RAY DIFFRACTION97.77
2.52-2.770.22631350.18142573X-RAY DIFFRACTION97.2
2.77-3.170.21371400.1692660X-RAY DIFFRACTION99.47
3.17-3.990.19351410.1482673X-RAY DIFFRACTION98.43
3.99-40.810.14941400.15512633X-RAY DIFFRACTION97.3

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