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- PDB-6t06: Crystal structure of YTHDC1 with fragment 19 (DHU_DC1_045) -

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Basic information

Entry
Database: PDB / ID: 6t06
TitleCrystal structure of YTHDC1 with fragment 19 (DHU_DC1_045)
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / Fragment / Complex / YTHDC1 / Epitranscriptomic
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / 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 / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / 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
3-imidazolidin-2-yl-2~{H}-indazole / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)42,6038
Polymers41,9342
Non-polymers6696
Water2,450136
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1593
Polymers20,9671
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4445
Polymers20,9671
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.364, 102.844, 42.033
Angle α, β, γ (deg.)90.000, 106.037, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-M5H / 3-imidazolidin-2-yl-2~{H}-indazole


Mass: 188.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
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: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40.5 Å / Num. obs: 11567 / % possible obs: 91.1 % / Redundancy: 2.99 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.15
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 1687 / CC1/2: 0.989

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Processing

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

4r3h


Resolution: 2.4→40.4 Å / SU ML: 0.353 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 27.9325
RfactorNum. reflection% reflection
Rfree0.2586 577 5 %
Rwork0.1765 --
obs0.1806 11545 91.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 39 136 2657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752582
X-RAY DIFFRACTIONf_angle_d0.95673495
X-RAY DIFFRACTIONf_chiral_restr0.0519385
X-RAY DIFFRACTIONf_plane_restr0.0052435
X-RAY DIFFRACTIONf_dihedral_angle_d9.00271814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.35081350.20212544X-RAY DIFFRACTION84.43
2.64-3.020.30281390.21262636X-RAY DIFFRACTION88.38
3.02-3.810.29531480.17112825X-RAY DIFFRACTION94.23
3.81-40.40.19291550.15852963X-RAY DIFFRACTION98.08

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