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- PDB-8bs4: Crystal structure of YTHDF1 YTH domain dimer -

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Basic information

Entry
Database: PDB / ID: 8bs4
TitleCrystal structure of YTHDF1 YTH domain dimer
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / YTHDF1 / Dimer / YTH / m6A
Function / homology
Function and homology information


regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability ...regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / positive regulation of translation / learning / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
ACETATE ION / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBedi, R.K. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of YTHDF1 YTH domain dimer
Authors: Bedi, R.K. / Caflisch, A.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1654
Polymers50,0142
Non-polymers1512
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint4 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.850, 91.850, 206.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-781-

HOH

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Components

#1: Protein YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 25007.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYJ9
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium citrate, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.926 Å / Num. obs: 31056 / % possible obs: 99.8 % / Redundancy: 16.13 % / Biso Wilson estimate: 49.85 Å2 / CC1/2: 1 / Net I/σ(I): 27.77
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 4849 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.83 Å / SU ML: 0.2905 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 1546 5 %
Rwork0.2145 29353 -
obs0.2161 30899 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 10 167 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763144
X-RAY DIFFRACTIONf_angle_d0.80624270
X-RAY DIFFRACTIONf_chiral_restr0.0531453
X-RAY DIFFRACTIONf_plane_restr0.0084559
X-RAY DIFFRACTIONf_dihedral_angle_d5.7152425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.37621350.3222552X-RAY DIFFRACTION98.07
2.17-2.240.35111380.30362627X-RAY DIFFRACTION99.68
2.24-2.330.33441380.28242601X-RAY DIFFRACTION99.56
2.33-2.440.31991370.27392618X-RAY DIFFRACTION99.78
2.44-2.570.30311390.25322629X-RAY DIFFRACTION99.53
2.57-2.730.341380.26142632X-RAY DIFFRACTION99.86
2.73-2.940.27411400.24242658X-RAY DIFFRACTION99.82
2.94-3.240.29631400.22092663X-RAY DIFFRACTION99.89
3.24-3.70.21981430.20142698X-RAY DIFFRACTION99.89
3.71-4.670.19691440.17162744X-RAY DIFFRACTION99.9
4.67-44.830.22691540.20732931X-RAY DIFFRACTION99.77

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