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- PDB-8q37: Crystal structure of YTHDC1 in complex with Compound 18 (ZA_312) -

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Basic information

Entry
Database: PDB / ID: 8q37
TitleCrystal structure of YTHDC1 in complex with Compound 18 (ZA_312)
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
Chem-IWF / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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)39,02412
Polymers37,6482
Non-polymers1,37610
Water5,459303
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5126
Polymers18,8241
Non-polymers6885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5126
Polymers18,8241
Non-polymers6885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.950, 103.550, 42.230
Angle α, β, γ (deg.)90.000, 104.730, 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-IWF / 2-chloranyl-9-[(2-methoxyphenyl)methyl]-~{N}-methyl-purin-6-amine


Mass: 303.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14ClN5O / 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.: 303 / 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: 45.19 %
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 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→38.64 Å / Num. obs: 83615 / % possible obs: 97.6 % / Redundancy: 3.41 % / Biso Wilson estimate: 20.57 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.85
Reflection shellResolution: 1.28→1.36 Å / Num. unique obs: 13331 / CC1/2: 0.426

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→38.64 Å / SU ML: 0.1971 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 4174 5 %
Rwork0.2107 79283 -
obs0.2118 83457 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.78 Å2
Refinement stepCycle: LAST / Resolution: 1.28→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 80 303 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652705
X-RAY DIFFRACTIONf_angle_d0.97973670
X-RAY DIFFRACTIONf_chiral_restr0.0873392
X-RAY DIFFRACTIONf_plane_restr0.0085456
X-RAY DIFFRACTIONf_dihedral_angle_d7.5674353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.50721270.50112399X-RAY DIFFRACTION89.35
1.29-1.310.43481400.46332661X-RAY DIFFRACTION98.59
1.31-1.320.42631410.41262687X-RAY DIFFRACTION98.54
1.32-1.340.38221390.38412634X-RAY DIFFRACTION98.58
1.34-1.360.41481410.36522667X-RAY DIFFRACTION98.35
1.36-1.380.36481380.35352634X-RAY DIFFRACTION97.64
1.38-1.40.39631390.32942642X-RAY DIFFRACTION97.89
1.4-1.420.33091390.3212637X-RAY DIFFRACTION97.03
1.42-1.440.33981370.32412589X-RAY DIFFRACTION96.29
1.44-1.460.33331320.31322522X-RAY DIFFRACTION93.68
1.46-1.490.32111420.28552686X-RAY DIFFRACTION99.16
1.49-1.520.25061420.25332701X-RAY DIFFRACTION99.54
1.52-1.540.2611400.23672678X-RAY DIFFRACTION99.58
1.54-1.580.25871430.22992712X-RAY DIFFRACTION99.65
1.58-1.610.24971420.22542687X-RAY DIFFRACTION99.54
1.61-1.650.24841400.22242668X-RAY DIFFRACTION99.15
1.65-1.690.2421400.21872660X-RAY DIFFRACTION98.49
1.69-1.730.2411420.21552696X-RAY DIFFRACTION98.54
1.73-1.790.21881380.22162618X-RAY DIFFRACTION97.94
1.79-1.840.25631400.22652656X-RAY DIFFRACTION97.49
1.84-1.910.24971380.21392619X-RAY DIFFRACTION96.33
1.91-1.990.22271320.21142503X-RAY DIFFRACTION92.95
1.99-2.080.23591410.20722674X-RAY DIFFRACTION98.81
2.08-2.190.22351400.20262678X-RAY DIFFRACTION98.98
2.19-2.320.24221410.2052694X-RAY DIFFRACTION98.78
2.32-2.50.22341410.20262686X-RAY DIFFRACTION98.33
2.5-2.750.2361380.20982635X-RAY DIFFRACTION98.47
2.75-3.150.22661410.20752672X-RAY DIFFRACTION97.64
3.15-3.970.21341370.17792592X-RAY DIFFRACTION94.49
3.97-38.640.19281430.18462696X-RAY DIFFRACTION97.86

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