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- PDB-8q4u: Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) -

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Basic information

Entry
Database: PDB / ID: 8q4u
TitleCrystal structure of YTHDC1 in complex with Compound 36 (ZA_540b)
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-JA0 / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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)39,00012
Polymers37,6482
Non-polymers1,35210
Water4,720262
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5006
Polymers18,8241
Non-polymers6765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5006
Polymers18,8241
Non-polymers6765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.100, 103.290, 42.160
Angle α, β, γ (deg.)90.000, 105.160, 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-JA0 / 9-[(3-chlorophenyl)methyl]-2-fluoranyl-~{N}-methyl-purin-6-amine


Mass: 291.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11ClFN5 / 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.: 262 / 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: 45.05 %
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: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→38.7 Å / Num. obs: 68786 / % possible obs: 98.4 % / Redundancy: 3.37 % / Biso Wilson estimate: 24.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2
Reflection shellResolution: 1.37→1.45 Å / Num. unique obs: 10882 / CC1/2: 0.647

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→38.7 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 3431 5 %
Rwork0.2123 65237 -
obs0.213 68668 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 1.37→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 80 262 2884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692698
X-RAY DIFFRACTIONf_angle_d0.85433664
X-RAY DIFFRACTIONf_chiral_restr0.0808394
X-RAY DIFFRACTIONf_plane_restr0.0076453
X-RAY DIFFRACTIONf_dihedral_angle_d6.9573351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.48881300.39362463X-RAY DIFFRACTION92.57
1.39-1.410.30181340.35322577X-RAY DIFFRACTION98.15
1.41-1.430.39581370.32862593X-RAY DIFFRACTION97.74
1.43-1.450.40421370.31232600X-RAY DIFFRACTION98.28
1.45-1.470.34561360.29772595X-RAY DIFFRACTION98.88
1.47-1.50.29711370.28392604X-RAY DIFFRACTION98.53
1.5-1.530.30281380.27652607X-RAY DIFFRACTION98.32
1.53-1.550.30251370.27542609X-RAY DIFFRACTION98.25
1.55-1.590.32151360.27552597X-RAY DIFFRACTION99.09
1.59-1.620.30421390.26222639X-RAY DIFFRACTION98.97
1.62-1.660.32461390.25682626X-RAY DIFFRACTION99.07
1.66-1.70.2981370.24852617X-RAY DIFFRACTION98.96
1.7-1.750.28061380.25152650X-RAY DIFFRACTION99.22
1.75-1.80.26341370.24822606X-RAY DIFFRACTION99.28
1.8-1.860.31131370.25132600X-RAY DIFFRACTION99.09
1.86-1.920.25941400.23942658X-RAY DIFFRACTION98.63
1.92-20.2881380.23382608X-RAY DIFFRACTION99.28
2-2.090.2191380.22412639X-RAY DIFFRACTION99.43
2.09-2.20.23031380.21922618X-RAY DIFFRACTION99.24
2.2-2.340.25831400.21652647X-RAY DIFFRACTION99.36
2.34-2.520.22851390.21332650X-RAY DIFFRACTION99.5
2.52-2.770.23961390.21742631X-RAY DIFFRACTION99.39
2.77-3.170.20481370.20892612X-RAY DIFFRACTION98.85
3.17-40.19331390.17692628X-RAY DIFFRACTION97.98
4-38.70.17151340.18432563X-RAY DIFFRACTION94.83

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