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- PDB-7z8w: Crystal structure of YTHDF2 with compound YLI_DC1_018 -

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Basic information

Entry
Database: PDB / ID: 7z8w
TitleCrystal structure of YTHDF2 with compound YLI_DC1_018
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 / regulation of hematopoietic stem cell differentiation / oocyte maturation / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / negative regulation of Notch signaling pathway / mRNA destabilization / mRNA catabolic process / humoral immune response / centriolar satellite / regulation of neurogenesis / 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
Chem-IHR / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 18, 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)40,09114
Polymers38,7362
Non-polymers1,35612
Water2,756153
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8375
Polymers19,3681
Non-polymers4694
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)20,2549
Polymers19,3681
Non-polymers8868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.950, 80.950, 112.930
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, 165 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IHR / ~{N}-cyclopropyl-3-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine


Mass: 189.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 55.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2 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: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.97 Å / Num. obs: 65399 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.73 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.8
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 10415 / CC1/2: 0.885

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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: 1.9→43.97 Å / SU ML: 0.2041 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 22.8927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 3269 5.01 %
Rwork0.1895 62039 -
obs0.1913 65308 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 87 153 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752524
X-RAY DIFFRACTIONf_angle_d0.8483417
X-RAY DIFFRACTIONf_chiral_restr0.0648349
X-RAY DIFFRACTIONf_plane_restr0.0078430
X-RAY DIFFRACTIONf_dihedral_angle_d18.2299343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.2491350.24382604X-RAY DIFFRACTION96.58
1.92-1.950.26621410.22222691X-RAY DIFFRACTION99.02
1.95-1.990.29711430.21832715X-RAY DIFFRACTION99.03
1.99-2.020.29391420.21152682X-RAY DIFFRACTION99.19
2.02-2.060.25261380.21292648X-RAY DIFFRACTION99.18
2.06-2.10.24551440.20742707X-RAY DIFFRACTION99.23
2.1-2.140.30961430.20792715X-RAY DIFFRACTION99.37
2.14-2.190.23541410.19042687X-RAY DIFFRACTION99.51
2.19-2.240.25341440.19052705X-RAY DIFFRACTION99.51
2.24-2.290.21151430.18942698X-RAY DIFFRACTION99.61
2.29-2.350.27651430.19842722X-RAY DIFFRACTION99.31
2.35-2.420.24031440.19942674X-RAY DIFFRACTION99.65
2.42-2.50.26321430.20462732X-RAY DIFFRACTION99.9
2.5-2.590.26871370.2022666X-RAY DIFFRACTION99.61
2.59-2.690.24181440.21332744X-RAY DIFFRACTION99.62
2.7-2.820.24581420.21482700X-RAY DIFFRACTION99.82
2.82-2.970.23071440.20142692X-RAY DIFFRACTION99.86
2.97-3.150.22071440.20282727X-RAY DIFFRACTION99.69
3.15-3.390.20861450.18422722X-RAY DIFFRACTION99.93
3.4-3.740.18061430.17352677X-RAY DIFFRACTION99.96
3.74-4.280.16591370.15672719X-RAY DIFFRACTION99.96
4.28-5.390.18551460.15362725X-RAY DIFFRACTION99.72
5.39-43.970.25461430.19332687X-RAY DIFFRACTION99.47

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