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- PDB-6yl9: Crystal structure of YTHDC1 with compound DHU_DC1_085 -

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Basic information

Entry
Database: PDB / ID: 6yl9
TitleCrystal structure of YTHDC1 with compound DHU_DC1_085
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-OXB / 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 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)42,93310
Polymers41,9342
Non-polymers9998
Water8,629479
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2554
Polymers20,9671
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6786
Polymers20,9671
Non-polymers7115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.740, 103.200, 42.400
Angle α, β, γ (deg.)90.000, 104.750, 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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OXB / 3-[(2~{R},5~{S})-2-(2,5-dimethylphenyl)-5-methyl-morpholin-4-yl]propane-1-sulfonamide


Mass: 326.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.01 Å3/Da / Density % sol: 38.65 %
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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→41 Å / Num. obs: 52073 / % possible obs: 97.6 % / Redundancy: 3.25 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.9
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8384 / CC1/2: 0.99

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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→41 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.126
RfactorNum. reflection% reflection
Rfree0.185 2603 5 %
Rwork0.1712 --
obs0.1719 52041 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 57 479 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532675
X-RAY DIFFRACTIONf_angle_d0.89993640
X-RAY DIFFRACTIONf_chiral_restr0.0802393
X-RAY DIFFRACTIONf_plane_restr0.0046454
X-RAY DIFFRACTIONf_dihedral_angle_d19.8497361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.21381330.19562537X-RAY DIFFRACTION94.68
1.52-1.550.24441360.18772604X-RAY DIFFRACTION98.6
1.55-1.580.19071390.18812633X-RAY DIFFRACTION98.72
1.58-1.620.20131370.18452608X-RAY DIFFRACTION98.85
1.62-1.660.2371390.18032633X-RAY DIFFRACTION98.58
1.66-1.70.20591370.18122597X-RAY DIFFRACTION98.38
1.7-1.740.19951370.18452612X-RAY DIFFRACTION98.25
1.74-1.790.2281380.18752609X-RAY DIFFRACTION98.11
1.79-1.850.18711340.18672554X-RAY DIFFRACTION96.14
1.85-1.920.2061370.17872597X-RAY DIFFRACTION97.89
1.92-20.21741370.17842612X-RAY DIFFRACTION98.25
2-2.090.1731380.16652606X-RAY DIFFRACTION97.97
2.09-2.20.19541370.1742602X-RAY DIFFRACTION97.96
2.2-2.330.18561370.17382617X-RAY DIFFRACTION97.9
2.33-2.510.18931370.17442598X-RAY DIFFRACTION97.09
2.51-2.770.2181330.18122522X-RAY DIFFRACTION95.4
2.77-3.170.18611370.1742609X-RAY DIFFRACTION97.97
3.17-3.990.14851400.15092640X-RAY DIFFRACTION98.2
3.99-410.16311400.15982648X-RAY DIFFRACTION97.86

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