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- PDB-8q2y: Crystal structure of YTHDC1 in complex with Compound 11 (ZA_572) -

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Basic information

Entry
Database: PDB / ID: 8q2y
TitleCrystal structure of YTHDC1 in complex with Compound 11 (ZA_572)
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader
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
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
Chem-IVI / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)38,7619
Polymers37,6482
Non-polymers1,1147
Water2,756153
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2373
Polymers18,8241
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5256
Polymers18,8241
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.910, 104.160, 41.880
Angle α, β, γ (deg.)90.000, 104.810, 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-IVI / 2-[2-chloranyl-6-(methylamino)purin-9-yl]-~{N}-phenyl-ethanamide


Mass: 316.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 44.98 %
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: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→40.49 Å / Num. obs: 35511 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.07
Reflection shellResolution: 1.71→1.81 Å / Num. unique obs: 5668 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→40.49 Å / SU ML: 0.3032 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257 1772 5 %
Rwork0.2259 33649 -
obs0.2275 35421 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.26 Å2
Refinement stepCycle: LAST / Resolution: 1.71→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 69 153 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812664
X-RAY DIFFRACTIONf_angle_d0.93443615
X-RAY DIFFRACTIONf_chiral_restr0.0585391
X-RAY DIFFRACTIONf_plane_restr0.0101451
X-RAY DIFFRACTIONf_dihedral_angle_d6.6592347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.46431340.42142554X-RAY DIFFRACTION96.59
1.75-1.810.38731360.3592574X-RAY DIFFRACTION99.45
1.81-1.860.37951360.32782582X-RAY DIFFRACTION99.49
1.86-1.930.36351360.33882589X-RAY DIFFRACTION98.77
1.93-2.010.39241370.29622590X-RAY DIFFRACTION99.31
2.01-2.10.28681370.26882610X-RAY DIFFRACTION99.78
2.1-2.210.32051360.27962589X-RAY DIFFRACTION99.71
2.21-2.350.26731370.27662584X-RAY DIFFRACTION98.62
2.35-2.530.30831360.24562586X-RAY DIFFRACTION99.56
2.53-2.780.29391380.25642619X-RAY DIFFRACTION99.24
2.78-3.190.32251360.24132580X-RAY DIFFRACTION98.91
3.19-4.010.23621360.19522590X-RAY DIFFRACTION98.55
4.02-40.490.1741370.17232602X-RAY DIFFRACTION97.79

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