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- PDB-9h2y: Crystal structure of YTHDC1 in complex with AI_056 -

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Basic information

Entry
Database: PDB / ID: 9h2y
TitleCrystal structure of YTHDC1 in complex with AI_056
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader
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
: / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsBedi, R.K. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of YTHDC1 in complex with AI_056
Authors: Bedi, R.K. / Caflisch, A.
History
DepositionOct 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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)38,61111
Polymers37,6482
Non-polymers9649
Water5,693316
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3706
Polymers18,8241
Non-polymers5465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2415
Polymers18,8241
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.850, 104.010, 41.990
Angle α, β, γ (deg.)90.000, 104.450, 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-A1IR4 / 3-sulfanyl-1,2,4-triazin-5-ol


Mass: 129.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H3N3OS / 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.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Feb 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→38.6 Å / Num. obs: 93468 / % possible obs: 99.2 % / Redundancy: 3.35 % / Biso Wilson estimate: 21.07 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.55
Reflection shellResolution: 1.24→1.31 Å / Num. unique obs: 15050 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→38.59 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.6419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 4666 5 %
Rwork0.2156 88674 -
obs0.2169 93340 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.19 Å2
Refinement stepCycle: LAST / Resolution: 1.24→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 54 316 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542598
X-RAY DIFFRACTIONf_angle_d0.76993527
X-RAY DIFFRACTIONf_chiral_restr0.0769384
X-RAY DIFFRACTIONf_plane_restr0.0077440
X-RAY DIFFRACTIONf_dihedral_angle_d12.0828927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.250.35681530.40212900X-RAY DIFFRACTION97.82
1.25-1.270.38771550.3852944X-RAY DIFFRACTION99.68
1.27-1.280.36091560.35472966X-RAY DIFFRACTION99.84
1.28-1.30.35231560.3452966X-RAY DIFFRACTION99.49
1.3-1.310.35161560.31732953X-RAY DIFFRACTION99.58
1.31-1.330.3441550.30572944X-RAY DIFFRACTION99.9
1.33-1.350.29841570.28322997X-RAY DIFFRACTION99.84
1.35-1.370.30661570.28592969X-RAY DIFFRACTION99.74
1.37-1.390.2921550.2772969X-RAY DIFFRACTION99.62
1.39-1.420.3061540.26922935X-RAY DIFFRACTION99.87
1.42-1.440.29941590.27463004X-RAY DIFFRACTION99.62
1.44-1.470.3111530.26552931X-RAY DIFFRACTION99.64
1.47-1.490.26891560.25132962X-RAY DIFFRACTION99.58
1.49-1.530.24051570.23292976X-RAY DIFFRACTION99.81
1.53-1.560.25611550.22782954X-RAY DIFFRACTION99.71
1.56-1.590.24291570.21892983X-RAY DIFFRACTION99.78
1.59-1.630.22121550.21862949X-RAY DIFFRACTION99.9
1.63-1.680.23341590.22043008X-RAY DIFFRACTION99.78
1.68-1.730.23941560.22122965X-RAY DIFFRACTION99.81
1.73-1.780.24191550.22862945X-RAY DIFFRACTION99.65
1.78-1.850.25341560.22812973X-RAY DIFFRACTION99.62
1.85-1.920.27391560.22192958X-RAY DIFFRACTION99.33
1.92-2.010.24231570.21852984X-RAY DIFFRACTION99.52
2.01-2.120.26171570.21052977X-RAY DIFFRACTION99.43
2.12-2.250.23031550.20882935X-RAY DIFFRACTION99.68
2.25-2.420.21961560.20422979X-RAY DIFFRACTION99.46
2.42-2.660.25961580.21632997X-RAY DIFFRACTION99.56
2.66-3.050.23871550.21342964X-RAY DIFFRACTION99.33
3.05-3.840.2261560.19342953X-RAY DIFFRACTION98.26
3.84-38.590.22341440.20062734X-RAY DIFFRACTION90.42

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