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- PDB-7p8f: Crystal structure of YTHDC1 with compound YLI_DC1_008 -

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Basic information

Entry
Database: PDB / ID: 7p8f
TitleCrystal structure of YTHDC1 with compound YLI_DC1_008
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / Inhibitor / complex / m6A
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 / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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 / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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-5ZK / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBedi, R.K. / Li, Y. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: Eur J Med Chem Rep / Year: 2022
Title: Structure-based design of ligands of the m6A-RNA reader YTHDC1
Authors: Li, Y. / Bedi, R.K. / Nai, F. / von Roten, V. / Dolbois, A. / Zalesak, F. / Nachawati, R. / Huang, D. / Caflisch, A.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)42,83710
Polymers41,9342
Non-polymers9038
Water6,990388
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2263
Polymers20,9671
Non-polymers2592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6117
Polymers20,9671
Non-polymers6436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.860, 103.740, 42.190
Angle α, β, γ (deg.)90.000, 106.349, 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: 20967.160 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-5ZK / ~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine


Mass: 163.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5 / 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.: 388 / 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 Å3/Da / Density % sol: 38.38 %
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 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.5 Å / Num. obs: 52624 / % possible obs: 99.3 % / Redundancy: 3.36 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 1 / Net I/σ(I): 22.72
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8389 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 1.5→40.48 Å / SU ML: 0.213 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.0517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2621 5 %
Rwork0.2088 49773 -
obs0.2099 52394 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 54 388 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062643
X-RAY DIFFRACTIONf_angle_d0.90043587
X-RAY DIFFRACTIONf_chiral_restr0.0842392
X-RAY DIFFRACTIONf_plane_restr0.0093446
X-RAY DIFFRACTIONf_dihedral_angle_d5.8843343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.38541310.34362492X-RAY DIFFRACTION94.01
1.52-1.550.26971380.31532611X-RAY DIFFRACTION99.03
1.55-1.580.28631360.30622582X-RAY DIFFRACTION98.84
1.58-1.620.30041370.28622621X-RAY DIFFRACTION99.32
1.62-1.660.29571380.27882631X-RAY DIFFRACTION98.86
1.66-1.70.29181370.26692609X-RAY DIFFRACTION98.99
1.7-1.740.3461380.26332625X-RAY DIFFRACTION99.17
1.74-1.80.34671380.25662598X-RAY DIFFRACTION99.31
1.8-1.850.33051380.25982631X-RAY DIFFRACTION99.39
1.85-1.920.28041390.24312632X-RAY DIFFRACTION99.28
1.92-20.28761380.25282624X-RAY DIFFRACTION99.6
2-2.090.24681380.22872629X-RAY DIFFRACTION99.53
2.09-2.20.28281390.23462630X-RAY DIFFRACTION99.32
2.2-2.330.24031390.23082642X-RAY DIFFRACTION99.43
2.33-2.510.27421370.22832610X-RAY DIFFRACTION99.38
2.52-2.770.27491390.22752628X-RAY DIFFRACTION99.46
2.77-3.170.23811390.20682645X-RAY DIFFRACTION99.68
3.17-3.990.19961400.17782666X-RAY DIFFRACTION99.61
3.99-40.480.15181420.15682667X-RAY DIFFRACTION99.19

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