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- PDB-7z4u: Crystal structure of YTHDF2 with compound YLI_DF_028 -

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Basic information

Entry
Database: PDB / ID: 7z4u
TitleCrystal structure of YTHDF2 with compound YLI_DF_028
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 / gamete generation / endothelial to hematopoietic transition / 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 / gamete generation / endothelial to hematopoietic transition / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity / negative regulation of stem cell differentiation / regulation of hematopoietic stem cell differentiation / oocyte maturation / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / mRNA destabilization / mRNA catabolic process / humoral immune response / regulation of neurogenesis / negative regulation of Notch signaling pathway / regulation of cell adhesion / regulation of mRNA stability / stress granule assembly / P-body / centriolar satellite / 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
6-cyclopropyl-3-methyl-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: 1.83 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 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 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)39,58010
Polymers38,7362
Non-polymers8448
Water2,234124
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7625
Polymers19,3681
Non-polymers3944
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)19,8185
Polymers19,3681
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.830, 80.830, 113.390
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 132 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FIQ / 6-cyclopropyl-3-methyl-1H-pyrimidine-2,4-dione


Mass: 166.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 5.1

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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: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→44.06 Å / Num. obs: 72603 / % possible obs: 99.8 % / Redundancy: 6.35 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.49
Reflection shellResolution: 1.83→1.94 Å / Num. unique obs: 11597 / CC1/2: 0.703

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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: 1.83→44.06 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 27.2861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 3626 5.01 %
Rwork0.2143 68769 -
obs0.2153 72395 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.84 Å2
Refinement stepCycle: LAST / Resolution: 1.83→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 51 124 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852479
X-RAY DIFFRACTIONf_angle_d0.96413361
X-RAY DIFFRACTIONf_chiral_restr0.0648349
X-RAY DIFFRACTIONf_plane_restr0.0078426
X-RAY DIFFRACTIONf_dihedral_angle_d11.0451336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.860.40031340.34462551X-RAY DIFFRACTION97.85
1.86-1.880.34451430.33182681X-RAY DIFFRACTION99.65
1.88-1.910.33191350.33442591X-RAY DIFFRACTION99.38
1.91-1.940.33421400.30192684X-RAY DIFFRACTION99.54
1.94-1.970.28721400.27732634X-RAY DIFFRACTION99.61
1.97-20.33121340.27672618X-RAY DIFFRACTION99.75
2-2.040.25721410.26552645X-RAY DIFFRACTION100
2.04-2.070.29751400.27122688X-RAY DIFFRACTION99.89
2.07-2.110.36751400.27442644X-RAY DIFFRACTION99.93
2.11-2.160.33881370.24762604X-RAY DIFFRACTION99.82
2.16-2.20.30251410.22522683X-RAY DIFFRACTION99.89
2.2-2.250.2351380.23982651X-RAY DIFFRACTION99.79
2.25-2.310.28811370.2372648X-RAY DIFFRACTION100
2.31-2.370.25691430.22712663X-RAY DIFFRACTION99.68
2.37-2.440.22341390.22832641X-RAY DIFFRACTION99.93
2.44-2.520.23111400.23062643X-RAY DIFFRACTION100
2.52-2.610.25261400.24442650X-RAY DIFFRACTION100
2.61-2.720.30161400.22892630X-RAY DIFFRACTION100
2.72-2.840.26671410.24142650X-RAY DIFFRACTION100
2.84-2.990.25391420.22152690X-RAY DIFFRACTION99.93
2.99-3.180.27881380.22442632X-RAY DIFFRACTION100
3.18-3.420.18951410.20972643X-RAY DIFFRACTION99.96
3.42-3.770.19821420.18232671X-RAY DIFFRACTION100
3.77-4.310.16371380.16752630X-RAY DIFFRACTION99.96
4.31-5.430.19531400.15812659X-RAY DIFFRACTION99.96
5.44-44.060.18141420.20072645X-RAY DIFFRACTION99.68

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