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- PDB-6zot: Crystal structure of YTHDF3 YTH domain in complex with m6A RNA -

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Basic information

Entry
Database: PDB / ID: 6zot
TitleCrystal structure of YTHDF3 YTH domain in complex with m6A RNA
Components
  • RNA
  • YTH domain-containing family protein 3
KeywordsRNA BINDING PROTEIN / YTHDF3 / m6A / complex
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
RNA / YTH domain-containing family protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBedi, R.K. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: J.Chem.Inf.Model. / Year: 2020
Title: Structural and Dynamic Insights into Redundant Function of YTHDF Proteins.
Authors: Li, Y. / Bedi, R.K. / Moroz-Omori, E.V. / Caflisch, A.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 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
B: YTH domain-containing family protein 3
A: YTH domain-containing family protein 3
C: RNA


Theoretical massNumber of molelcules
Total (without water)48,1713
Polymers48,1713
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.750, 100.750, 72.880
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-649-

HOH

21A-650-

HOH

31C-101-

HOH

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Components

#1: Protein YTH domain-containing family protein 3


Mass: 23285.250 Da / Num. of mol.: 2
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: RNA chain RNA


Mass: 1600.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 0.1M Tris pH8, 0.2M NaCl

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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: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.06 Å / Num. obs: 10844 / % possible obs: 99.8 % / Redundancy: 14.95 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.25
Reflection shellResolution: 2.7→2.86 Å / Num. unique obs: 1696 / CC1/2: 0.617

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCI

4rci


Resolution: 2.7→45.06 Å / SU ML: 0.4001 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2757 541 5.01 %
Rwork0.2153 10257 -
obs0.2182 10798 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 82 0 105 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082795
X-RAY DIFFRACTIONf_angle_d1.44453805
X-RAY DIFFRACTIONf_chiral_restr0.0929408
X-RAY DIFFRACTIONf_plane_restr0.0091480
X-RAY DIFFRACTIONf_dihedral_angle_d18.8099388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.421320.2982507X-RAY DIFFRACTION99.43
2.97-3.40.29811320.23252506X-RAY DIFFRACTION99.92
3.4-4.280.22341340.19042551X-RAY DIFFRACTION99.81
4.28-45.060.25321430.19772693X-RAY DIFFRACTION99.72

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