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- PDB-7l4x: YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA join... -

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Basic information

Entry
Database: PDB / ID: 7l4x
TitleYTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by two six-bp DNA duplexes in P3221 Crystal
Components
  • YTH domain-containing protein 1
  • ssDNA w/N6A
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 / 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
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
B: YTH domain-containing protein 1
E: ssDNA w/N6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0015
Polymers22,8142
Non-polymers1863
Water1,856103
1
B: YTH domain-containing protein 1
E: ssDNA w/N6A
hetero molecules

E: ssDNA w/N6A

E: ssDNA w/N6A


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers30,7964
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)56.744, 56.744, 108.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-778-

HOH

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Components

#1: 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
#2: DNA chain ssDNA w/N6A


Mass: 3990.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% v/v 2-propanol, 0.1M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate pH 4.6

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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→36.49 Å / Num. obs: 19738 / % possible obs: 99.8 % / Redundancy: 17.5 % / Biso Wilson estimate: 35.37 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.024 / Net I/σ(I): 17.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1934 / CC1/2: 0.508 / Rpim(I) all: 0.537

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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→36.49 Å / SU ML: 0.2278 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 990 5.02 %
Rwork0.1986 18712 -
obs0.2003 19702 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.89 Å2
Refinement stepCycle: LAST / Resolution: 1.79→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1302 265 12 103 1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361653
X-RAY DIFFRACTIONf_angle_d0.70582283
X-RAY DIFFRACTIONf_chiral_restr0.0445246
X-RAY DIFFRACTIONf_plane_restr0.0047243
X-RAY DIFFRACTIONf_dihedral_angle_d17.966644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.890.38341410.33352607X-RAY DIFFRACTION98.99
1.89-20.27761390.23782620X-RAY DIFFRACTION100
2-2.160.29091430.24362635X-RAY DIFFRACTION100
2.16-2.380.28811370.22052658X-RAY DIFFRACTION100
2.38-2.720.24351430.23142670X-RAY DIFFRACTION99.86
2.72-3.430.23941370.22462695X-RAY DIFFRACTION99.96
3.43-36.490.19631500.15722827X-RAY DIFFRACTION99.8

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