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- PDB-8q2s: Crystal structure of YTHDC1 in complex with Compound 4 (ZA_232) -

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Basic information

Entry
Database: PDB / ID: 8q2s
TitleCrystal structure of YTHDC1 in complex with Compound 4 (ZA_232)
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}-methyl-9-phenyl-purin-6-amine / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBedi, R.K. / Zalesak, F. / 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)38,74310
Polymers37,6482
Non-polymers1,0968
Water7,855436
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3725
Polymers18,8241
Non-polymers5484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3725
Polymers18,8241
Non-polymers5484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.910, 103.680, 42.090
Angle α, β, γ (deg.)90.000, 105.120, 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-IU2 / 2-chloranyl-~{N}-methyl-9-phenyl-purin-6-amine


Mass: 259.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10ClN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
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: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→40.63 Å / Num. obs: 62590 / % possible obs: 97.9 % / Redundancy: 3.45 % / Biso Wilson estimate: 18.38 Å2 / CC1/2: 0.996 / Net I/σ(I): 15.16
Reflection shellResolution: 1.41→1.49 Å / Num. unique obs: 9875 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→40.63 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 3128 5 %
Rwork0.1971 59389 -
obs0.1985 62517 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.03 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 66 436 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622682
X-RAY DIFFRACTIONf_angle_d0.87943648
X-RAY DIFFRACTIONf_chiral_restr0.085395
X-RAY DIFFRACTIONf_plane_restr0.0076455
X-RAY DIFFRACTIONf_dihedral_angle_d6.2805350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.39881350.38162561X-RAY DIFFRACTION93.29
1.43-1.450.35961380.33642608X-RAY DIFFRACTION93.91
1.45-1.480.31191420.32696X-RAY DIFFRACTION98.68
1.48-1.50.33851420.25762712X-RAY DIFFRACTION99.44
1.5-1.530.32781450.23862751X-RAY DIFFRACTION99.35
1.53-1.560.2751430.22912708X-RAY DIFFRACTION99.3
1.56-1.60.27351450.21522759X-RAY DIFFRACTION99.35
1.6-1.640.26531420.20022697X-RAY DIFFRACTION99.23
1.64-1.680.22631430.20462738X-RAY DIFFRACTION99.07
1.68-1.720.24041430.20652713X-RAY DIFFRACTION98.72
1.72-1.770.27261430.21762700X-RAY DIFFRACTION98.41
1.77-1.830.26631420.22582711X-RAY DIFFRACTION98.21
1.83-1.90.21761410.2122664X-RAY DIFFRACTION96.89
1.9-1.970.2381370.20122603X-RAY DIFFRACTION95.07
1.97-2.060.21141430.19662720X-RAY DIFFRACTION99.13
2.06-2.170.21371460.19012778X-RAY DIFFRACTION99.9
2.17-2.310.23661440.19232731X-RAY DIFFRACTION99.58
2.31-2.480.22211460.18982774X-RAY DIFFRACTION99.42
2.48-2.730.24141420.20122708X-RAY DIFFRACTION98.99
2.73-3.130.23081430.1972701X-RAY DIFFRACTION97.53
3.13-3.940.17951370.17012602X-RAY DIFFRACTION93.83
3.94-40.630.19841460.17792754X-RAY DIFFRACTION98.04

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