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- PDB-6t09: Crystal structure of YTHDC1 with fragment 24 (PSI_DC1_003) -

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Basic information

Entry
Database: PDB / ID: 6t09
TitleCrystal structure of YTHDC1 with fragment 24 (PSI_DC1_003)
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / Fragment / Complex / YTHDC1 / Epitranscriptomic
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
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}-pyridin-3-ylethanamide / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBedi, R.K. / Huang, D. / Sledz, P. / Caflisch, A.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments.
Authors: Bedi, R.K. / Huang, D. / Wiedmer, L. / Li, Y. / Dolbois, A. / Wojdyla, J.A. / Sharpe, M.E. / Caflisch, A. / Sledz, P.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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)42,87911
Polymers41,9342
Non-polymers9459
Water6,413356
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5847
Polymers20,9671
Non-polymers6166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2954
Polymers20,9671
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.668, 103.261, 42.138
Angle α, β, γ (deg.)90.000, 105.561, 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-M4T / ~{N}-pyridin-3-ylethanamide


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


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.: 356 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
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 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40.6 Å / Num. obs: 61712 / % possible obs: 94.8 % / Redundancy: 1.75 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 9458 / CC1/2: 0.438

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.75→40.59 Å / SU ML: 0.2323 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.9788
RfactorNum. reflection% reflection
Rfree0.225 1999 6.11 %
Rwork0.1876 --
obs0.1899 32728 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 55 356 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612630
X-RAY DIFFRACTIONf_angle_d0.87873560
X-RAY DIFFRACTIONf_chiral_restr0.0545386
X-RAY DIFFRACTIONf_plane_restr0.0058446
X-RAY DIFFRACTIONf_dihedral_angle_d8.2362117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.33381330.29822138X-RAY DIFFRACTION97.22
1.79-1.840.32111480.26882200X-RAY DIFFRACTION99.79
1.84-1.90.27241480.25212160X-RAY DIFFRACTION99.48
1.9-1.960.28371330.24672179X-RAY DIFFRACTION99.78
1.96-2.030.29761510.22162190X-RAY DIFFRACTION99.28
2.03-2.110.28081380.20312211X-RAY DIFFRACTION99.66
2.11-2.210.24741490.19442204X-RAY DIFFRACTION99.83
2.21-2.320.21961420.19042182X-RAY DIFFRACTION99.87
2.32-2.470.25111400.17932215X-RAY DIFFRACTION99.87
2.47-2.660.22661440.19182188X-RAY DIFFRACTION99.79
2.66-2.920.22751400.18762197X-RAY DIFFRACTION99.83
2.92-3.350.21881450.18252202X-RAY DIFFRACTION99.75
3.35-4.220.18211410.15622227X-RAY DIFFRACTION100
4.22-40.590.18421470.16422236X-RAY DIFFRACTION99.75

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