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- PDB-7z92: Crystal structure of YTHDF2 with compound YLI_DF_024 -

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Basic information

Entry
Database: PDB / ID: 7z92
TitleCrystal structure of YTHDF2 with compound YLI_DF_024
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / Epitranscriptomic reader / m6A reader
Function / homology
Function and homology information


C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / gamete generation / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity ...C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / gamete generation / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity / negative regulation of stem cell differentiation / oocyte maturation / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / humoral immune response / regulation of neurogenesis / centriolar satellite / regulation of cell adhesion / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / innate immune response / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
5-azanyl-3,6-dimethyl-1H-pyrimidine-2,4-dione / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsNai, F. / Li, Y. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B-189363 Switzerland
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Fragment Ligands of the m 6 A-RNA Reader YTHDF2.
Authors: Nai, F. / Nachawati, R. / Zalesak, F. / Wang, X. / Li, Y. / Caflisch, A.
History
DepositionMar 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing family protein 2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5269
Polymers38,7362
Non-polymers7917
Water1,76598
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7154
Polymers19,3681
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8115
Polymers19,3681
Non-polymers4434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.120, 80.120, 113.850
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 2 / CLL-associated antigen KW-14 / High-glucose-regulated protein 8 / Renal carcinoma antigen NY-REN-2


Mass: 19367.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF2, HGRG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5A9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IGT / 5-azanyl-3,6-dimethyl-1H-pyrimidine-2,4-dione


Mass: 155.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.05 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 5.2

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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: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→44.01 Å / Num. obs: 62701 / % possible obs: 99.4 % / Redundancy: 3.77 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.11
Reflection shellResolution: 1.91→2.03 Å / Num. unique obs: 10116 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RDN

4rdn


Resolution: 1.91→44.01 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 25.52
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 3136 5.01 %
Rwork0.2107 59439 -
obs0.2118 62575 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.2 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 47 98 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722439
X-RAY DIFFRACTIONf_angle_d0.85073306
X-RAY DIFFRACTIONf_chiral_restr0.0626344
X-RAY DIFFRACTIONf_plane_restr0.0077419
X-RAY DIFFRACTIONf_dihedral_angle_d6.02323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.940.29181400.28292678X-RAY DIFFRACTION97.01
1.94-1.980.29021410.27452688X-RAY DIFFRACTION99.75
1.98-2.010.2811470.2652740X-RAY DIFFRACTION99.76
2.01-2.050.31181420.24342698X-RAY DIFFRACTION99.75
2.05-2.090.30621440.26352686X-RAY DIFFRACTION99.86
2.09-2.130.24471400.25182725X-RAY DIFFRACTION99.83
2.13-2.180.32161430.24362747X-RAY DIFFRACTION99.9
2.18-2.230.25641440.24052702X-RAY DIFFRACTION99.82
2.23-2.280.25811420.24122723X-RAY DIFFRACTION99.93
2.28-2.340.26851420.22482683X-RAY DIFFRACTION99.72
2.34-2.410.2371430.23172716X-RAY DIFFRACTION99.76
2.41-2.490.26581460.23082733X-RAY DIFFRACTION99.52
2.49-2.580.27681430.24492698X-RAY DIFFRACTION99.89
2.58-2.680.28171450.23972725X-RAY DIFFRACTION99.79
2.68-2.80.26641410.24312697X-RAY DIFFRACTION99.96
2.8-2.950.26111440.22252700X-RAY DIFFRACTION99.65
2.95-3.140.24321410.23582689X-RAY DIFFRACTION99.72
3.14-3.380.22211430.20322714X-RAY DIFFRACTION99.37
3.38-3.720.2111440.17592695X-RAY DIFFRACTION99.51
3.72-4.260.17461420.16772677X-RAY DIFFRACTION98.67
4.26-5.360.1931430.16612677X-RAY DIFFRACTION97.71
5.37-44.010.20791360.20262648X-RAY DIFFRACTION97.82

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