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- PDB-8q2q: Crystal structure of YTHDC1 in complex with Compound 2b (YL_32) -

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Basic information

Entry
Database: PDB / ID: 8q2q
TitleCrystal structure of YTHDC1 in complex with Compound 2b (YL_32)
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader
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
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
2-chloranyl-~{N},9-dimethyl-purin-6-amine / 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. / Li, Y. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Design of a Potent and Selective YTHDC1 Ligand.
Authors: Zalesak, F. / Nai, F. / Herok, M. / Bochenkova, E. / Bedi, R.K. / Li, Y. / Errani, F. / Caflisch, A.
History
DepositionAug 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81112
Polymers37,6482
Non-polymers1,16410
Water7,260403
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3105
Polymers18,8241
Non-polymers4864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5027
Polymers18,8241
Non-polymers6786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.980, 103.410, 42.390
Angle α, β, γ (deg.)90.000, 106.000, 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 YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 18823.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-IT6 / 2-chloranyl-~{N},9-dimethyl-purin-6-amine


Mass: 197.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8ClN5 / 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.: 403 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 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: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40.75 Å / Num. obs: 81179 / % possible obs: 99.3 % / Redundancy: 3.35 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.18
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 12993 / CC1/2: 0.692

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40.75 Å / SU ML: 0.1658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 4041 5 %
Rwork0.2157 76738 -
obs0.2163 80779 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.82 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 66 403 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652715
X-RAY DIFFRACTIONf_angle_d0.94353681
X-RAY DIFFRACTIONf_chiral_restr0.0851394
X-RAY DIFFRACTIONf_plane_restr0.0089458
X-RAY DIFFRACTIONf_dihedral_angle_d5.8109352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.39251270.40972432X-RAY DIFFRACTION91.95
1.31-1.330.47591410.38572683X-RAY DIFFRACTION99.12
1.33-1.350.38931380.38832612X-RAY DIFFRACTION98.99
1.35-1.360.36011400.35782659X-RAY DIFFRACTION99.08
1.36-1.380.37071390.35622642X-RAY DIFFRACTION99
1.38-1.40.35541370.33912606X-RAY DIFFRACTION98.35
1.4-1.420.31961390.32872654X-RAY DIFFRACTION98.73
1.42-1.440.36781380.31152614X-RAY DIFFRACTION99.28
1.44-1.470.35421410.30282677X-RAY DIFFRACTION99.23
1.47-1.490.29551400.28982652X-RAY DIFFRACTION99.25
1.49-1.520.31171390.2672637X-RAY DIFFRACTION99.36
1.52-1.550.25841390.25362652X-RAY DIFFRACTION99.04
1.55-1.580.26121390.25672624X-RAY DIFFRACTION99.39
1.58-1.620.26341410.25222676X-RAY DIFFRACTION99.4
1.62-1.650.28721390.24542653X-RAY DIFFRACTION99.15
1.65-1.690.26841400.24662648X-RAY DIFFRACTION99.29
1.69-1.740.26941390.23532647X-RAY DIFFRACTION99.25
1.74-1.790.2871390.24622638X-RAY DIFFRACTION99.46
1.79-1.850.28371410.2512665X-RAY DIFFRACTION98.98
1.85-1.920.25961410.23532681X-RAY DIFFRACTION99.72
1.92-1.990.23371390.22782644X-RAY DIFFRACTION99.25
1.99-2.080.18541390.21372640X-RAY DIFFRACTION99.75
2.08-2.190.23861400.21422666X-RAY DIFFRACTION99.57
2.19-2.330.22181420.21242683X-RAY DIFFRACTION99.72
2.33-2.510.23311400.21552672X-RAY DIFFRACTION99.15
2.51-2.760.23781390.21892641X-RAY DIFFRACTION99.11
2.76-3.160.21591400.2092650X-RAY DIFFRACTION99.29
3.16-3.980.19541420.18182690X-RAY DIFFRACTION99.06
3.98-40.750.1561430.16142700X-RAY DIFFRACTION99.37

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