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- PDB-6we8: YTH domain of human YTHDC1 -

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Basic information

Entry
Database: PDB / ID: 6we8
TitleYTH domain of human YTHDC1
ComponentsYTH domain-containing protein 1
KeywordsDNA BINDING PROTEIN / N6-methyladenine binding protein domain
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
YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
Authors: Woodcock, C.B. / Horton, J.R. / Zhou, J. / Bedford, M.T. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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
B: YTH domain-containing protein 1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81317
Polymers37,6482
Non-polymers1,16515
Water6,954386
1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,51810
Polymers18,8241
Non-polymers6959
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2947
Polymers18,8241
Non-polymers4706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: YTH domain-containing protein 1
hetero molecules

A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81317
Polymers37,6482
Non-polymers1,16515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area3740 Å2
ΔGint-58 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.914, 103.960, 42.201
Angle α, β, γ (deg.)90.000, 104.869, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1-0.15M ammonium sulfate 0.1 M Bis-Tris pH 5.5 25-29% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→20.01 Å / Num. obs: 93137 / % possible obs: 86.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.05 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.038 / Net I/σ(I): 22.2
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2859 / CC1/2: 0.41 / CC star: 0.763 / Rpim(I) all: 0.517 / % possible all: 26.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.18→20.01 Å / SU ML: 0.0923 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1947 2019 2.17 %
Rwork0.1657 91005 -
obs0.1664 93024 86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.47 Å2
Refinement stepCycle: LAST / Resolution: 1.18→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 68 386 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232769
X-RAY DIFFRACTIONf_angle_d0.57763746
X-RAY DIFFRACTIONf_chiral_restr0.0677402
X-RAY DIFFRACTIONf_plane_restr0.0035473
X-RAY DIFFRACTIONf_dihedral_angle_d17.1711020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.4424380.34051739X-RAY DIFFRACTION23.1
1.21-1.240.26690.2793011X-RAY DIFFRACTION40.05
1.24-1.280.29511140.24265028X-RAY DIFFRACTION66.52
1.28-1.320.27261670.21956753X-RAY DIFFRACTION89.85
1.32-1.370.22711420.1997292X-RAY DIFFRACTION96.46
1.37-1.420.24771750.18837428X-RAY DIFFRACTION98.4
1.42-1.490.21281530.16267424X-RAY DIFFRACTION98.5
1.49-1.570.18021630.14597367X-RAY DIFFRACTION97.49
1.57-1.670.17291680.14267504X-RAY DIFFRACTION99.28
1.67-1.790.19011680.14837479X-RAY DIFFRACTION99.11
1.79-1.970.17341620.15097485X-RAY DIFFRACTION99
1.97-2.260.19021600.15197440X-RAY DIFFRACTION97.95
2.26-2.850.18351700.17037558X-RAY DIFFRACTION99.52
2.85-20.010.18441700.16327497X-RAY DIFFRACTION98.23

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