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- PDB-6rt5: The YTH domain of YTHDC1 protein in complex with Gm6AC oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 6rt5
TitleThe YTH domain of YTHDC1 protein in complex with Gm6AC 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 / 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
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: 2.303 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
A: RNA (5'-R(*(6MZ)P*C)-3')
B: YTH domain-containing protein 1
C: YTH domain-containing protein 1
E: RNA (5'-R(*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8337
Polymers39,5454
Non-polymers2883
Water2,972165
1
A: RNA (5'-R(*(6MZ)P*C)-3')
C: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9654
Polymers19,7722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
E: RNA (5'-R(*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8693
Polymers19,7722
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.787, 103.655, 41.779
Angle α, β, γ (deg.)90.00, 104.76, 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: 948.663 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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion
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 PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.3→40.41 Å / Num. obs: 14246 / % possible obs: 97.8 % / Redundancy: 4.48 % / CC1/2: 0.999 / Rrim(I) all: 0.043 / Net I/σ(I): 26.26
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.5 % / Num. unique obs: 2119 / CC1/2: 0.988 / Rrim(I) all: 0.147 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 2.303→40.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.2748 712 5.01 %
Rwork0.2086 --
obs0.2118 14225 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.303→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 72 15 165 2693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072591
X-RAY DIFFRACTIONf_angle_d0.9113532
X-RAY DIFFRACTIONf_dihedral_angle_d8.4311763
X-RAY DIFFRACTIONf_chiral_restr0.05401
X-RAY DIFFRACTIONf_plane_restr0.005432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3027-2.48040.35081350.23412564X-RAY DIFFRACTION93
2.4804-2.730.29311430.23762716X-RAY DIFFRACTION100
2.73-3.12490.31521450.23212753X-RAY DIFFRACTION100
3.1249-3.93650.26961430.21232706X-RAY DIFFRACTION98
3.9365-40.40640.23531460.18022774X-RAY DIFFRACTION99

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