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- PDB-6rt6: The YTH domain of YTHDC1 protein in complex with GGm6AC oligonucl... -

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Basic information

Entry
Database: PDB / ID: 6rt6
TitleThe YTH domain of YTHDC1 protein in complex with GGm6AC 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 / 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
RNA / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 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)40,6208
Polymers40,2354
Non-polymers3844
Water5,801322
1
B: YTH domain-containing protein 1
E: RNA (5'-R(*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2143
Polymers20,1182
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-27 kcal/mol
Surface area7910 Å2
MethodPISA
2
A: RNA (5'-R(*(6MZ)P*C)-3')
C: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4065
Polymers20,1182
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-20 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.913, 103.739, 41.983
Angle α, β, γ (deg.)90.00, 104.50, 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: 1293.869 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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
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 25% 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: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 1.46→40.66 Å / Num. obs: 56905 / % possible obs: 99.4 % / Redundancy: 3.36 % / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 12.33
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9052 / CC1/2: 0.379 / Rrim(I) all: 1.691 / % possible all: 97.9

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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: 1.461→40.645 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.22 2004 3.52 %
Rwork0.2063 --
obs0.2068 56867 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.461→40.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 64 20 322 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062645
X-RAY DIFFRACTIONf_angle_d0.8393597
X-RAY DIFFRACTIONf_dihedral_angle_d11.1891211
X-RAY DIFFRACTIONf_chiral_restr0.08403
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4605-1.49710.36561420.40613821X-RAY DIFFRACTION97
1.4971-1.53750.38051370.36813876X-RAY DIFFRACTION99
1.5375-1.58280.36151460.33733884X-RAY DIFFRACTION99
1.5828-1.63390.33781380.29943923X-RAY DIFFRACTION100
1.6339-1.69230.30921450.28473940X-RAY DIFFRACTION100
1.6923-1.760.30141470.25753910X-RAY DIFFRACTION100
1.76-1.84010.27051380.24333943X-RAY DIFFRACTION100
1.8401-1.93710.26911420.233929X-RAY DIFFRACTION100
1.9371-2.05850.24491470.21213931X-RAY DIFFRACTION100
2.0585-2.21740.24971370.20563949X-RAY DIFFRACTION100
2.2174-2.44060.25241450.19933907X-RAY DIFFRACTION100
2.4406-2.79360.22871440.2033956X-RAY DIFFRACTION100
2.7936-3.51940.19121450.18743928X-RAY DIFFRACTION100
3.5194-40.66060.15591510.16623966X-RAY DIFFRACTION99

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