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- PDB-8q4w: Crystal structure of YTHDC1 in complex with Compound 40 (CS_3a) -

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Basic information

Entry
Database: PDB / ID: 8q4w
TitleCrystal structure of YTHDC1 in complex with Compound 40 (CS_3a)
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-JNC / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 7, 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)38,7449
Polymers37,6482
Non-polymers1,0977
Water3,567198
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3244
Polymers18,8241
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4205
Polymers18,8241
Non-polymers5964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.840, 103.970, 42.070
Angle α, β, γ (deg.)90.000, 104.420, 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-JNC / 5-chloranyl-3-[(3-chlorophenyl)methyl]-~{N}-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine


Mass: 308.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11Cl2N5 / 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.: 198 / 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: 45.12 %
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: 1.61→38.589 Å / Num. obs: 42700 / % possible obs: 99.1 % / Redundancy: 3.39 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.68
Reflection shellResolution: 1.61→1.7 Å / Num. unique obs: 6828 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→38.58 Å / SU ML: 0.1864 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 2131 5 %
Rwork0.2064 40496 -
obs0.208 42627 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.33 Å2
Refinement stepCycle: LAST / Resolution: 1.61→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 65 198 2778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622647
X-RAY DIFFRACTIONf_angle_d0.79973595
X-RAY DIFFRACTIONf_chiral_restr0.0512391
X-RAY DIFFRACTIONf_plane_restr0.0068448
X-RAY DIFFRACTIONf_dihedral_angle_d13.3977923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.2951380.29462619X-RAY DIFFRACTION97.87
1.65-1.690.29931440.28012719X-RAY DIFFRACTION99.72
1.69-1.730.31971430.26932727X-RAY DIFFRACTION99.83
1.73-1.780.3311410.25682690X-RAY DIFFRACTION99.51
1.78-1.840.2931420.27012702X-RAY DIFFRACTION99.75
1.84-1.910.30981440.25332732X-RAY DIFFRACTION99.45
1.91-1.980.27731410.24382677X-RAY DIFFRACTION99.33
1.98-2.070.27521420.2292698X-RAY DIFFRACTION99.44
2.07-2.180.23761430.22292707X-RAY DIFFRACTION99.3
2.18-2.320.26681410.22422703X-RAY DIFFRACTION99.58
2.32-2.50.26151430.21692725X-RAY DIFFRACTION99.62
2.5-2.750.21771420.22912685X-RAY DIFFRACTION99.33
2.75-3.150.25721420.22372709X-RAY DIFFRACTION98.96
3.15-3.960.21841420.18122688X-RAY DIFFRACTION97.96
3.96-38.580.20441430.17292715X-RAY DIFFRACTION98.01

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