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- PDB-6sz3: Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158) -

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Basic information

Entry
Database: PDB / ID: 6sz3
TitleCrystal structure of YTHDC1 with fragment 4 (DHU_DC1_158)
ComponentsYTH domain-containing protein 1
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
~{N}-methyl-5,6,7,8-tetrahydroquinolin-4-amine / 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. / 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 1, 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)42,7399
Polymers41,9342
Non-polymers8057
Water9,098505
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0632
Polymers20,9671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6767
Polymers20,9671
Non-polymers7096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.655, 103.447, 42.225
Angle α, β, γ (deg.)90.000, 105.893, 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-M1H / ~{N}-methyl-5,6,7,8-tetrahydroquinolin-4-amine


Mass: 162.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
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: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→40.611 Å / Num. obs: 156810 / % possible obs: 94.7 % / Redundancy: 1.74 % / Biso Wilson estimate: 15.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.06
Reflection shellResolution: 1.28→1.36 Å / Num. unique obs: 24690 / CC1/2: 0.43

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Processing

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

4r3h


Resolution: 1.28→40.61 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7741
RfactorNum. reflection% reflection
Rfree0.2053 2004 2.42 %
Rwork0.1942 --
obs0.1944 82975 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.53 Å2
Refinement stepCycle: LAST / Resolution: 1.28→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 49 505 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492642
X-RAY DIFFRACTIONf_angle_d0.78593577
X-RAY DIFFRACTIONf_chiral_restr0.0794386
X-RAY DIFFRACTIONf_plane_restr0.0042447
X-RAY DIFFRACTIONf_dihedral_angle_d11.63711548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.411330.35185515X-RAY DIFFRACTION94.75
1.31-1.350.33471390.32255753X-RAY DIFFRACTION99.83
1.35-1.390.2941440.29175806X-RAY DIFFRACTION99.93
1.39-1.430.28321520.27235787X-RAY DIFFRACTION99.88
1.43-1.490.25511430.25415818X-RAY DIFFRACTION99.87
1.49-1.550.23871270.22045805X-RAY DIFFRACTION99.66
1.55-1.620.21951560.20525773X-RAY DIFFRACTION99.95
1.62-1.70.23471450.19925829X-RAY DIFFRACTION99.97
1.7-1.810.26931430.19935814X-RAY DIFFRACTION99.88
1.81-1.950.20271470.18945791X-RAY DIFFRACTION99.9
1.95-2.140.21551390.18165816X-RAY DIFFRACTION99.73
2.14-2.450.18551400.185819X-RAY DIFFRACTION99.53
2.45-3.090.18741510.18875815X-RAY DIFFRACTION99.62
3.09-40.60.16281450.16535830X-RAY DIFFRACTION99.02

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