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- PDB-6yni: Crystal structure of YTHDC1 with compound DHU_DC1_036 -

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Basic information

Entry
Database: PDB / ID: 6yni
TitleCrystal structure of YTHDC1 with compound DHU_DC1_036
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-P0Q / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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)43,37414
Polymers41,9342
Non-polymers1,44012
Water8,071448
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3515
Polymers20,9671
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0239
Polymers20,9671
Non-polymers1,0568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.250, 103.040, 42.040
Angle α, β, γ (deg.)90.000, 106.545, 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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P0Q / (2~{R},3~{R})-2-(3-chlorophenyl)-3,5,5-trimethyl-morpholine


Mass: 239.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18ClNO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
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 / 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: 1.36→40.3 Å / Num. obs: 67741 / % possible obs: 99.2 % / Redundancy: 2.97 % / Biso Wilson estimate: 15.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.48
Reflection shellResolution: 1.36→1.44 Å / Num. unique obs: 10880 / CC1/2: 0.658

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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: 1.36→40.3 Å / SU ML: 0.1609 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 3387 5 %
Rwork0.1912 64350 -
obs0.1928 67737 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.13 Å2
Refinement stepCycle: LAST / Resolution: 1.36→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 82 448 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482737
X-RAY DIFFRACTIONf_angle_d0.79833726
X-RAY DIFFRACTIONf_chiral_restr0.0743401
X-RAY DIFFRACTIONf_plane_restr0.0051461
X-RAY DIFFRACTIONf_dihedral_angle_d25.7561363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.41111340.3582546X-RAY DIFFRACTION96.06
1.38-1.40.36291430.35042717X-RAY DIFFRACTION99.31
1.4-1.420.37561400.33272652X-RAY DIFFRACTION99.43
1.42-1.450.331420.31552698X-RAY DIFFRACTION99.16
1.45-1.470.38061400.31122655X-RAY DIFFRACTION99.47
1.47-1.50.33241400.28432672X-RAY DIFFRACTION99.47
1.5-1.530.27671410.26792678X-RAY DIFFRACTION99.51
1.53-1.560.25791410.24692675X-RAY DIFFRACTION99.26
1.56-1.590.2811410.23742665X-RAY DIFFRACTION99.4
1.59-1.630.22741430.21372725X-RAY DIFFRACTION99.69
1.63-1.670.22781410.20842668X-RAY DIFFRACTION99.68
1.67-1.720.22471410.20152676X-RAY DIFFRACTION99.68
1.72-1.770.23441410.19842678X-RAY DIFFRACTION99.4
1.77-1.820.2111420.19782695X-RAY DIFFRACTION99.79
1.82-1.890.25141410.19782686X-RAY DIFFRACTION99.82
1.89-1.960.22511430.1872710X-RAY DIFFRACTION99.83
1.96-2.050.21961410.17872679X-RAY DIFFRACTION99.79
2.05-2.160.19131410.17662681X-RAY DIFFRACTION99.51
2.16-2.30.21011400.17982682X-RAY DIFFRACTION99.23
2.3-2.480.1961430.18382705X-RAY DIFFRACTION99.37
2.48-2.720.2441400.19882658X-RAY DIFFRACTION99.26
2.72-3.120.23271420.18452698X-RAY DIFFRACTION99.68
3.12-3.930.17681430.15532718X-RAY DIFFRACTION99.37
3.93-40.30.18991430.15992733X-RAY DIFFRACTION99.62

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