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- PDB-8bs5: Crystal structure of YTHDF3 YTH domain open conformation -

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Basic information

Entry
Database: PDB / ID: 8bs5
TitleCrystal structure of YTHDF3 YTH domain open conformation
ComponentsYTH domain-containing family protein 3
KeywordsRNA BINDING PROTEIN / YTHDF3 / YTH / m6A
Function / homology
Function and homology information


organelle assembly / regulation of trophoblast cell migration / N6-methyladenosine-containing RNA reader activity / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / positive regulation of translational initiation / regulation of mRNA stability / stress granule assembly / positive regulation of translation / P-body ...organelle assembly / regulation of trophoblast cell migration / N6-methyladenosine-containing RNA reader activity / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / positive regulation of translational initiation / regulation of mRNA stability / stress granule assembly / positive regulation of translation / P-body / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / YTH domain-containing family protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 YTHDF3 YTH domain open conformation
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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3553
Polymers23,0991
Non-polymers2562
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.860, 80.860, 122.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-602-

PEG

21A-737-

HOH

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Components

#1: Protein YTH domain-containing family protein 3 / DF3


Mass: 23099.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z739
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium sodium tartrate tetrahydrate, 20% 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 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→48.73 Å / Num. obs: 14732 / % possible obs: 99.5 % / Redundancy: 12.81 % / Biso Wilson estimate: 35.3 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.23
Reflection shellResolution: 2.49→2.64 Å / Num. unique obs: 2250 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→41.77 Å / SU ML: 0.3204 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3056 731 4.99 %
Rwork0.2751 13911 -
obs0.2765 14642 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.71 Å2
Refinement stepCycle: LAST / Resolution: 2.49→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 17 50 1361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071349
X-RAY DIFFRACTIONf_angle_d0.88791830
X-RAY DIFFRACTIONf_chiral_restr0.0571195
X-RAY DIFFRACTIONf_plane_restr0.0063236
X-RAY DIFFRACTIONf_dihedral_angle_d7.4229180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.690.33961390.31512652X-RAY DIFFRACTION97.62
2.69-2.960.3521440.28862733X-RAY DIFFRACTION99.31
2.96-3.380.31271440.2772756X-RAY DIFFRACTION99.28
3.39-4.260.29331470.2512796X-RAY DIFFRACTION99.46
4.26-41.770.28681570.27852974X-RAY DIFFRACTION99.81

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