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- PDB-6ykj: Crystal structure of YTHDC1 with compound DHU_DC1_125 -

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Basic information

Entry
Database: PDB / ID: 6ykj
TitleCrystal structure of YTHDC1 with compound DHU_DC1_125
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
~{N}-methyl-4-(methylamino)pyridine-2-carboxamide / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 6, 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)42,7459
Polymers41,9342
Non-polymers8117
Water7,386410
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3244
Polymers20,9671
Non-polymers3573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4215
Polymers20,9671
Non-polymers4534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.650, 103.170, 42.210
Angle α, β, γ (deg.)90.000, 105.769, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OUW / ~{N}-methyl-4-(methylamino)pyridine-2-carboxamide


Mass: 165.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 1.98 Å3/Da / Density % sol: 37.92 %
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: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.63 Å / Num. obs: 41940 / % possible obs: 97.5 % / Redundancy: 3.35 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.72
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 6714 / CC1/2: 0.6

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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: 1.6→40.62 Å / SU ML: 0.203 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.0993
RfactorNum. reflection% reflection
Rfree0.2541 2077 5 %
Rwork0.2088 --
obs0.2111 41506 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 49 410 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622629
X-RAY DIFFRACTIONf_angle_d0.84953564
X-RAY DIFFRACTIONf_chiral_restr0.0533388
X-RAY DIFFRACTIONf_plane_restr0.0051448
X-RAY DIFFRACTIONf_dihedral_angle_d17.814344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33551340.28682560X-RAY DIFFRACTION94.76
1.64-1.680.33371410.27482667X-RAY DIFFRACTION98.49
1.68-1.720.3151410.26412691X-RAY DIFFRACTION98.81
1.72-1.780.2861410.24792677X-RAY DIFFRACTION98.95
1.78-1.830.28741420.24312698X-RAY DIFFRACTION99.16
1.83-1.90.41241320.30612505X-RAY DIFFRACTION92.79
1.9-1.970.36551330.34282518X-RAY DIFFRACTION92.31
1.97-2.060.28191410.21572671X-RAY DIFFRACTION99.19
2.06-2.170.26751410.20452693X-RAY DIFFRACTION99.3
2.17-2.310.40391240.28012350X-RAY DIFFRACTION86.62
2.31-2.490.22071430.20362708X-RAY DIFFRACTION99.1
2.49-2.740.2631390.21112644X-RAY DIFFRACTION98.3
2.74-3.130.25631400.19332664X-RAY DIFFRACTION97.73
3.13-3.950.19641410.16892667X-RAY DIFFRACTION97.16
3.95-40.620.17791440.15752716X-RAY DIFFRACTION98.65

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