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- PDB-6rt4: The YTH domain of YTHDC1 protein in complex with m6ACU oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 6rt4
TitleThe YTH domain of YTHDC1 protein in complex with m6ACU oligonucleotide
Components
  • RNA (5'-R(*(6MZ)P*C)-3')
  • YTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / Protein-RNA interaction / epitranscriptomics
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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
RNA / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBedi, R. / Sledz, P. / Caflisch, A.
CitationJournal: J Chem Theory Comput / Year: 2019
Title: Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif.
Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Huang, D. / Sledz, P. / Caflisch, A.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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

Downloads & links

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Assembly

Deposited unit
C: RNA (5'-R(*(6MZ)P*C)-3')
B: YTH domain-containing protein 1
A: YTH domain-containing protein 1
D: RNA (5'-R(*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,04310
Polymers39,4674
Non-polymers5766
Water5,909328
1
C: RNA (5'-R(*(6MZ)P*C)-3')
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1186
Polymers19,7332
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
D: RNA (5'-R(*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9264
Polymers19,7332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.105, 103.503, 41.955
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(*(6MZ)P*C)-3')


Mass: 909.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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 (E. coli) / References: UniProt: Q96MU7
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris at pH 6.5, 0.2 M ammonium sulfate and 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 1.49→38.87 Å / Num. obs: 53214 / % possible obs: 95.1 % / Redundancy: 3.47 % / CC1/2: 0.999 / Rrim(I) all: 0.037 / Net I/σ(I): 17.15
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 3.26 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8210 / CC1/2: 0.885 / Rrim(I) all: 0.597 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 1.49→38.794 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.37
RfactorNum. reflection% reflection
Rfree0.2302 2006 3.77 %
Rwork0.2043 --
obs0.2053 53206 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→38.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 84 30 328 2963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052717
X-RAY DIFFRACTIONf_angle_d0.7853686
X-RAY DIFFRACTIONf_dihedral_angle_d9.8311553
X-RAY DIFFRACTIONf_chiral_restr0.078409
X-RAY DIFFRACTIONf_plane_restr0.005448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4855-1.52270.38231280.35343241X-RAY DIFFRACTION87
1.5227-1.56380.37031410.31593710X-RAY DIFFRACTION99
1.5638-1.60990.31031580.28923714X-RAY DIFFRACTION100
1.6099-1.66180.28821320.2613684X-RAY DIFFRACTION99
1.6618-1.72120.28561500.25383670X-RAY DIFFRACTION99
1.7212-1.79010.29631440.24063677X-RAY DIFFRACTION98
1.7901-1.87160.31731460.24493577X-RAY DIFFRACTION97
1.8716-1.97030.28211410.23223700X-RAY DIFFRACTION99
1.9703-2.09370.26351430.22623751X-RAY DIFFRACTION99
2.0937-2.25540.24581450.2193711X-RAY DIFFRACTION99
2.2554-2.48230.23121390.21073721X-RAY DIFFRACTION99
2.4823-2.84140.20691380.21263627X-RAY DIFFRACTION97
2.8414-3.57940.18941520.19363715X-RAY DIFFRACTION99
3.5794-38.80690.21421490.16433702X-RAY DIFFRACTION98

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