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- PDB-8bs6: Crystal structure of YTHDF3 disulfide mutant (closed conformation) -

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Basic information

Entry
Database: PDB / ID: 8bs6
TitleCrystal structure of YTHDF3 disulfide mutant (closed conformation)
ComponentsYTH domain-containing family protein 3
KeywordsRNA BINDING PROTEIN / YTHDF3 / mutant / disulfide / 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
YTH domain-containing family protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBedi, R.K. / Li, Y. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of YTHDF3 disulfide mutant (closed conformation)
Authors: Bedi, R.K. / Li, Y. / Caflisch, A.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing family protein 3


Theoretical massNumber of molelcules
Total (without water)25,5081
Polymers25,5081
Non-polymers00
Water5,260292
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)61.900, 61.900, 81.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
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,z+1/2

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Components

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


Mass: 25507.803 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.78 Å3/Da / Density % sol: 30.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 2M Disodium malonate

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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: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→44.83 Å / Num. obs: 55256 / % possible obs: 100 % / Redundancy: 8.36 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.83
Reflection shellResolution: 1.2→1.27 Å / Num. unique obs: 8867 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→32.52 Å / SU ML: 0.131 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 2756 5 %
Rwork0.1792 52380 -
obs0.1802 55136 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.73 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 0 292 1842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541688
X-RAY DIFFRACTIONf_angle_d0.86282301
X-RAY DIFFRACTIONf_chiral_restr0.0845240
X-RAY DIFFRACTIONf_plane_restr0.0069303
X-RAY DIFFRACTIONf_dihedral_angle_d5.6025236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.26551390.28572636X-RAY DIFFRACTION99.78
1.22-1.250.28181370.26972604X-RAY DIFFRACTION99.71
1.25-1.270.2641370.2612603X-RAY DIFFRACTION99.71
1.27-1.290.27081370.23512596X-RAY DIFFRACTION99.78
1.29-1.320.20981360.23492611X-RAY DIFFRACTION99.78
1.32-1.350.23381380.21852617X-RAY DIFFRACTION99.96
1.35-1.390.25691380.2152627X-RAY DIFFRACTION99.89
1.39-1.430.2241370.20712597X-RAY DIFFRACTION99.93
1.43-1.470.21891380.20242617X-RAY DIFFRACTION99.96
1.47-1.510.2281380.19362622X-RAY DIFFRACTION99.96
1.51-1.570.2261360.18672587X-RAY DIFFRACTION99.93
1.57-1.630.19971390.18392639X-RAY DIFFRACTION99.96
1.63-1.710.20561380.1782618X-RAY DIFFRACTION99.93
1.71-1.80.1791370.17972609X-RAY DIFFRACTION100
1.8-1.910.19591380.17972605X-RAY DIFFRACTION100
1.91-2.060.19761380.16782624X-RAY DIFFRACTION100
2.06-2.260.2141370.16412616X-RAY DIFFRACTION100
2.26-2.590.17281380.17332644X-RAY DIFFRACTION100
2.59-3.260.18191390.17262645X-RAY DIFFRACTION100
3.26-32.520.17631410.14722663X-RAY DIFFRACTION99.96

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