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- PDB-7l4y: YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA join... -

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Basic information

Entry
Database: PDB / ID: 7l4y
TitleYTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by Two Six-bp DNA Duplexes in P212121 Crystal
Components
  • YTH domain-containing protein 1
  • ssDNA 13mer
KeywordsDNA BINDING PROTEIN/DNA / N6-METHYLADENINE BINDING PROTEIN DOMAIN / SSDNA / DNA BINDING PROTEIN / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN-DNA complex
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
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.
Authors: Yu, D. / Horton, J.R. / Yang, J. / Hajian, T. / Vedadi, M. / Sagum, C.A. / Bedford, M.T. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: ssDNA 13mer
B: YTH domain-containing protein 1
E: ssDNA 13mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8674
Polymers26,8053
Non-polymers621
Water1,58588
1
F: ssDNA 13mer
B: YTH domain-containing protein 1
E: ssDNA 13mer
hetero molecules

F: ssDNA 13mer


Theoretical massNumber of molelcules
Total (without water)30,8585
Polymers30,7964
Non-polymers621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)45.968, 66.383, 77.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: DNA chain ssDNA 13mer


Mass: 3990.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 18823.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q96MU7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% v/v 2-propanol, 26% PEG 400, and 0.1M sodium citrate tribasic dihydrate pH 5.0

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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: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→39.55 Å / Num. obs: 20038 / % possible obs: 86.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 30.09 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Net I/σ(I): 21.6
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 872 / CC1/2: 0.738 / Rpim(I) all: 0.382 / % possible all: 38.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WEA

6wea


Resolution: 1.79→39.55 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 998 5 %
Rwork0.207 18975 -
obs0.2087 19973 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.57 Å2
Refinement stepCycle: LAST / Resolution: 1.79→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 530 4 88 1920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271938
X-RAY DIFFRACTIONf_angle_d0.58682728
X-RAY DIFFRACTIONf_chiral_restr0.0379292
X-RAY DIFFRACTIONf_plane_restr0.0036256
X-RAY DIFFRACTIONf_dihedral_angle_d20.7619778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.880.3937690.32311303X-RAY DIFFRACTION42.02
1.88-20.3091210.2872323X-RAY DIFFRACTION75.29
2-2.150.30541530.27362894X-RAY DIFFRACTION93.78
2.15-2.370.27781570.2333000X-RAY DIFFRACTION96.05
2.37-2.710.27351630.23793087X-RAY DIFFRACTION99.02
2.71-3.420.27921620.21663093X-RAY DIFFRACTION97.57
3.42-39.550.18231730.16753275X-RAY DIFFRACTION98.71

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