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- PDB-6szr: Crystal structure of YTHDC1 with fragment 9 (DHU_DC1_107) -

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Basic information

Entry
Database: PDB / ID: 6szr
TitleCrystal structure of YTHDC1 with fragment 9 (DHU_DC1_107)
ComponentsYTH domain-containing protein 1
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
Chem-M3Z / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBedi, R.K. / Huang, D. / Sledz, P. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_180345 Switzerland
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

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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)42,7569
Polymers41,9342
Non-polymers8227
Water7,945441
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2554
Polymers20,9671
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5015
Polymers20,9671
Non-polymers5334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.508, 103.290, 41.947
Angle α, β, γ (deg.)90.000, 105.399, 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: 20967.160 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-M3Z / 6-[[methyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione


Mass: 245.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 1.97 Å3/Da / Density % sol: 37.49 %
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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→40.6 Å / Num. obs: 39367 / % possible obs: 99.1 % / Redundancy: 3.42 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.09
Reflection shellResolution: 1.64→1.74 Å / Num. unique obs: 6195 / CC1/2: 0.405

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 1.64→40.44 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 2007 5.1 %
Rwork0.1924 37321 -
obs0.1947 39328 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 1.64→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 48 441 3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592644
X-RAY DIFFRACTIONf_angle_d0.75923582
X-RAY DIFFRACTIONf_chiral_restr0.0528392
X-RAY DIFFRACTIONf_plane_restr0.0051446
X-RAY DIFFRACTIONf_dihedral_angle_d8.1332150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.32671380.3332504X-RAY DIFFRACTION94.26
1.68-1.730.35061500.31872668X-RAY DIFFRACTION99.61
1.73-1.780.32621400.282642X-RAY DIFFRACTION99.57
1.78-1.830.27491430.25922704X-RAY DIFFRACTION99.55
1.83-1.90.28061450.23262670X-RAY DIFFRACTION99.72
1.9-1.980.29461400.22412684X-RAY DIFFRACTION99.51
1.98-2.070.26791490.20282667X-RAY DIFFRACTION99.65
2.07-2.180.26711380.18992648X-RAY DIFFRACTION99.64
2.18-2.310.26431390.17892686X-RAY DIFFRACTION99.54
2.31-2.490.20621470.1712686X-RAY DIFFRACTION99.68
2.49-2.740.20891360.18812668X-RAY DIFFRACTION99.64
2.74-3.140.2461500.1782670X-RAY DIFFRACTION99.79
3.14-3.950.19011420.16222721X-RAY DIFFRACTION99.55
3.95-40.440.21791500.16792703X-RAY DIFFRACTION99.51

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