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- PDB-6ym8: Crystal structure of YTHDC1 with compound YLI_DC1_002 -

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Basic information

Entry
Database: PDB / ID: 6ym8
TitleCrystal structure of YTHDC1 with compound YLI_DC1_002
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
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
2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine / 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. / Wiedmer, L. / Caflisch, A.
Funding support Switzerland, Sweden, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
Swedish Research CouncilVR 2019-00608 Sweden
CitationJournal: To Be Published
Title: Crystal structure of YTHDC1 with compound YLI_DC1_002
Authors: Bedi, R.K. / Li, Y. / Wiedmer, L. / Caflisch, A.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTHDC1
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7829
Polymers41,9342
Non-polymers8487
Water8,629479
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2473
Polymers20,9671
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5356
Polymers20,9671
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.810, 103.600, 42.030
Angle α, β, γ (deg.)90.000, 105.656, 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-OYN / 2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine


Mass: 183.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6ClN5 / 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.: 479 / 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: 38.2 %
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 / Detector: PIXEL / Date: Jan 30, 2020
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: 52060 / % possible obs: 99.6 % / Redundancy: 4.52 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.56
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8327 / CC1/2: 0.767

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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: 1.5→38.33 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6871
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 2599 5 %
Rwork0.1857 49357 -
obs0.1872 51956 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.96 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 49 479 3066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532668
X-RAY DIFFRACTIONf_angle_d0.7693618
X-RAY DIFFRACTIONf_chiral_restr0.0532392
X-RAY DIFFRACTIONf_plane_restr0.005449
X-RAY DIFFRACTIONf_dihedral_angle_d17.8278346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.36281320.28042500X-RAY DIFFRACTION96.59
1.53-1.560.23371360.27412584X-RAY DIFFRACTION99.27
1.56-1.590.31691360.25672586X-RAY DIFFRACTION99.23
1.59-1.620.30011340.24862553X-RAY DIFFRACTION99.59
1.62-1.660.28281390.23812635X-RAY DIFFRACTION99.57
1.66-1.70.2991350.22692566X-RAY DIFFRACTION99.48
1.7-1.750.27351370.22372599X-RAY DIFFRACTION99.74
1.75-1.80.22511360.2172582X-RAY DIFFRACTION99.6
1.8-1.860.26861370.20622603X-RAY DIFFRACTION100
1.86-1.930.25541380.19512624X-RAY DIFFRACTION99.96
1.93-20.24511370.19312607X-RAY DIFFRACTION99.82
2-2.090.21961380.18532610X-RAY DIFFRACTION100
2.09-2.20.20431370.17962608X-RAY DIFFRACTION99.96
2.2-2.340.21921380.18082613X-RAY DIFFRACTION99.75
2.34-2.520.23391350.18022575X-RAY DIFFRACTION99.78
2.52-2.780.21621380.18572620X-RAY DIFFRACTION99.86
2.78-3.180.19981380.18092618X-RAY DIFFRACTION100
3.18-40.16351380.16282619X-RAY DIFFRACTION99.78
4-38.330.19321400.15812655X-RAY DIFFRACTION99.79

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