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- PDB-7pj8: Crystal structure of YTHDC1 with compound DHU_DC1_225 -

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Basic information

Entry
Database: PDB / ID: 7pj8
TitleCrystal structure of YTHDC1 with compound DHU_DC1_225
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 / 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
N-methyl-1H-indole-4-carboxamide / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBedi, R.K. / Huang, D. / 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
DepositionAug 23, 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

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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)42,95511
Polymers41,9342
Non-polymers1,0219
Water7,981443
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5266
Polymers20,9671
Non-polymers5585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4305
Polymers20,9671
Non-polymers4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.560, 103.070, 42.170
Angle α, β, γ (deg.)90.000, 106.009, 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-7RT / N-methyl-1H-indole-4-carboxamide


Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
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, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40.54 Å / Num. obs: 61197 / % possible obs: 96.6 % / Redundancy: 3.44 % / Biso Wilson estimate: 20.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.69
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 9612 / CC1/2: 0.785

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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: 1.4→40.53 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 3054 5 %
Rwork0.1943 58031 -
obs0.1955 61085 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 61 443 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562679
X-RAY DIFFRACTIONf_angle_d0.87513626
X-RAY DIFFRACTIONf_chiral_restr0.0817390
X-RAY DIFFRACTIONf_plane_restr0.0079452
X-RAY DIFFRACTIONf_dihedral_angle_d7.1018345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.41331260.39522406X-RAY DIFFRACTION88.9
1.43-1.450.41111370.3522608X-RAY DIFFRACTION94.95
1.45-1.470.321370.32422596X-RAY DIFFRACTION96.37
1.47-1.50.28061400.29092657X-RAY DIFFRACTION97.22
1.5-1.530.31621400.26762651X-RAY DIFFRACTION97.35
1.53-1.560.28461400.25552660X-RAY DIFFRACTION97.39
1.56-1.590.26791390.23542634X-RAY DIFFRACTION97.64
1.59-1.630.26281400.22462658X-RAY DIFFRACTION96.75
1.63-1.670.27451380.22082632X-RAY DIFFRACTION96.95
1.67-1.720.24081370.21832599X-RAY DIFFRACTION95.07
1.72-1.770.24231390.22222625X-RAY DIFFRACTION96.31
1.77-1.830.24111400.22062669X-RAY DIFFRACTION98.08
1.83-1.890.26131420.21362681X-RAY DIFFRACTION98.4
1.89-1.970.2331410.21412677X-RAY DIFFRACTION97.58
1.97-2.060.2231380.20052650X-RAY DIFFRACTION97.62
2.06-2.160.22271400.19322664X-RAY DIFFRACTION97.23
2.16-2.30.23291390.19762633X-RAY DIFFRACTION96.55
2.3-2.480.20551350.19042570X-RAY DIFFRACTION93.31
2.48-2.730.22571400.20332680X-RAY DIFFRACTION98.7
2.73-3.120.20261420.19762681X-RAY DIFFRACTION97.92
3.12-3.930.17051420.16452705X-RAY DIFFRACTION97.87
3.93-40.530.19321420.15752695X-RAY DIFFRACTION97.12

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