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- PDB-9h2w: Crystal structure of YTHDC1 in complex with AI_055 -

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Basic information

Entry
Database: PDB / ID: 9h2w
TitleCrystal structure of YTHDC1 in complex with AI_055
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: 1.28 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_04
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)38,59310
Polymers37,6482
Non-polymers9458
Water6,864381
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2004
Polymers18,8241
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3926
Polymers18,8241
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.760, 103.648, 41.868
Angle α, β, γ (deg.)90.000, 104.418, 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-A1IR5 / 2-sulfanyl-3~{H}-thieno[2,3-d]pyrimidin-4-one


Mass: 184.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2OS2 / 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.: 381 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
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: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.28→40.55 Å / Num. obs: 150574 / % possible obs: 90.2 % / Redundancy: 1.56 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.75
Reflection shellResolution: 1.28→1.35 Å / Num. unique obs: 22160 / CC1/2: 0.472

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→40.55 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 4077 5.06 %
Rwork0.1976 76427 -
obs0.1988 80504 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.28→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 52 381 2963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062668
X-RAY DIFFRACTIONf_angle_d0.76733622
X-RAY DIFFRACTIONf_chiral_restr0.0764393
X-RAY DIFFRACTIONf_plane_restr0.0064450
X-RAY DIFFRACTIONf_dihedral_angle_d12.3376950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.37821420.33942537X-RAY DIFFRACTION92.76
1.3-1.310.34051430.3312579X-RAY DIFFRACTION94.15
1.31-1.330.32081450.32512607X-RAY DIFFRACTION94.77
1.33-1.340.33531340.30382599X-RAY DIFFRACTION94.67
1.34-1.360.36251250.29742629X-RAY DIFFRACTION94.9
1.36-1.380.29361400.28922621X-RAY DIFFRACTION95.37
1.38-1.40.35141230.28052655X-RAY DIFFRACTION95.37
1.4-1.430.28531170.26782615X-RAY DIFFRACTION95.22
1.43-1.450.2891310.25962637X-RAY DIFFRACTION95.65
1.45-1.470.26971590.24752643X-RAY DIFFRACTION95.83
1.47-1.50.30041340.23652603X-RAY DIFFRACTION95.6
1.5-1.530.24181530.21972642X-RAY DIFFRACTION95.88
1.53-1.560.23491420.21412586X-RAY DIFFRACTION94.33
1.56-1.590.25571240.20412654X-RAY DIFFRACTION95.33
1.59-1.630.22411410.21162630X-RAY DIFFRACTION96.99
1.63-1.670.22591360.21162723X-RAY DIFFRACTION96.72
1.67-1.720.25921350.20772619X-RAY DIFFRACTION95.49
1.72-1.770.23461340.21642667X-RAY DIFFRACTION96.59
1.77-1.830.24931410.2172692X-RAY DIFFRACTION97.45
1.83-1.890.25821440.2062687X-RAY DIFFRACTION97.69
1.89-1.970.23291240.20312701X-RAY DIFFRACTION97.68
1.97-2.060.19851340.20062697X-RAY DIFFRACTION97.69
2.06-2.160.2171680.19222672X-RAY DIFFRACTION97.29
2.16-2.30.22621740.18532669X-RAY DIFFRACTION97.13
2.3-2.480.21251620.192653X-RAY DIFFRACTION96.7
2.48-2.730.21431440.19882591X-RAY DIFFRACTION94.47
2.73-3.120.22291400.19912638X-RAY DIFFRACTION95.17
3.12-3.930.20281300.17012620X-RAY DIFFRACTION94.02
3.93-40.550.18121580.17112561X-RAY DIFFRACTION91.77

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