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- PDB-6ynp: Crystal structure of YTHDC1 with compound T96C1 -

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Basic information

Entry
Database: PDB / ID: 6ynp
TitleCrystal structure of YTHDC1 with compound T96C1
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / 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 / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / 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
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
~{N}-methylpyridine-3-carboxamide / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBedi, R.K. / Huang, D. / Wiedmer, L. / 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
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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: YTHDC1
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,91512
Polymers41,9342
Non-polymers98010
Water11,277626
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4886
Polymers20,9671
Non-polymers5205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4276
Polymers20,9671
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.620, 103.290, 42.300
Angle α, β, γ (deg.)90.000, 105.491, 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 YTHDC1 /


Mass: 20967.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-PJH / ~{N}-methylpyridine-3-carboxamide / Nicotinyl methylamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 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: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→40.8 Å / Num. obs: 131690 / % possible obs: 99.5 % / Redundancy: 4.29 % / Biso Wilson estimate: 12.16 Å2 / CC1/2: 1 / Net I/σ(I): 15.08
Reflection shellResolution: 1.1→1.17 Å / Num. unique obs: 20992 / CC1/2: 0.613

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.1→40.76 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 6574 5 %
Rwork0.1913 124855 -
obs0.1917 131429 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.72 Å2
Refinement stepCycle: LAST / Resolution: 1.1→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 56 626 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482779
X-RAY DIFFRACTIONf_angle_d0.81093787
X-RAY DIFFRACTIONf_chiral_restr0.0788407
X-RAY DIFFRACTIONf_plane_restr0.0048478
X-RAY DIFFRACTIONf_dihedral_angle_d23.394378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.35442020.33183855X-RAY DIFFRACTION92.23
1.11-1.130.32372200.32254163X-RAY DIFFRACTION99.3
1.13-1.140.28942180.30234152X-RAY DIFFRACTION99.32
1.14-1.150.30512180.29544133X-RAY DIFFRACTION99.7
1.15-1.170.30482170.29094119X-RAY DIFFRACTION99.47
1.17-1.190.26262200.27394197X-RAY DIFFRACTION99.39
1.19-1.20.2712200.26144162X-RAY DIFFRACTION99.59
1.2-1.220.25272150.25154086X-RAY DIFFRACTION99.56
1.22-1.240.28712240.25154257X-RAY DIFFRACTION99.62
1.24-1.260.24142160.24514111X-RAY DIFFRACTION99.75
1.26-1.280.25212210.23854193X-RAY DIFFRACTION99.55
1.28-1.30.24232180.23054137X-RAY DIFFRACTION99.57
1.3-1.330.24632190.22544160X-RAY DIFFRACTION99.77
1.33-1.360.21672190.21594167X-RAY DIFFRACTION99.77
1.36-1.390.20172200.20884177X-RAY DIFFRACTION99.89
1.39-1.420.24132220.20534212X-RAY DIFFRACTION99.42
1.42-1.450.20872170.20114128X-RAY DIFFRACTION99.86
1.45-1.490.22092190.1944163X-RAY DIFFRACTION99.82
1.49-1.540.19922200.18284169X-RAY DIFFRACTION99.77
1.54-1.590.20032210.18344198X-RAY DIFFRACTION99.91
1.59-1.640.20932190.17894164X-RAY DIFFRACTION99.64
1.64-1.710.18412200.17664185X-RAY DIFFRACTION99.84
1.71-1.790.20112190.18424160X-RAY DIFFRACTION99.84
1.79-1.880.1942220.18084203X-RAY DIFFRACTION99.84
1.88-20.20162190.1814174X-RAY DIFFRACTION99.86
2-2.150.16722210.17654186X-RAY DIFFRACTION99.86
2.15-2.370.20342210.18034201X-RAY DIFFRACTION99.89
2.37-2.710.19432210.18824192X-RAY DIFFRACTION99.73
2.71-3.420.17512210.1744199X-RAY DIFFRACTION99.84
3.42-40.760.15452250.16274252X-RAY DIFFRACTION99.8

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