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- PDB-7z54: Crystal structure of YTHDF2 with compound YLI_DC1_006 -

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Basic information

Entry
Database: PDB / ID: 7z54
TitleCrystal structure of YTHDF2 with compound YLI_DC1_006
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 / positive regulation of cap-independent translational initiation / regulation of rRNA processing / 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 / positive regulation of cap-independent translational initiation / regulation of rRNA processing / gamete generation / endothelial to hematopoietic transition / 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 / mRNA catabolic process / humoral immune response / negative regulation of Notch signaling pathway / regulation of neurogenesis / 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 / cytoplasm / cytosol
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
9-cyclopropyl-~{N}-methyl-purin-6-amine / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsNai, F. / Li, Y. / Dolbois, A. / 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 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 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)40,04215
Polymers38,7362
Non-polymers1,30613
Water3,027168
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,19610
Polymers19,3681
Non-polymers8299
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)19,8455
Polymers19,3681
Non-polymers4774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.580, 80.580, 113.380
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, 181 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-OYT / 9-cyclopropyl-~{N}-methyl-purin-6-amine


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.05 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: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→40.29 Å / Num. obs: 37653 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.05
Reflection shellResolution: 1.82→1.93 Å / Num. unique obs: 6032 / CC1/2: 0.963

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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: 1.82→40.29 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.9504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1877 4.99 %
Rwork0.1926 35710 -
obs0.1942 37587 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.56 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 77 168 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682492
X-RAY DIFFRACTIONf_angle_d0.84873381
X-RAY DIFFRACTIONf_chiral_restr0.0638347
X-RAY DIFFRACTIONf_plane_restr0.0072427
X-RAY DIFFRACTIONf_dihedral_angle_d6.8852335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.29461440.23842724X-RAY DIFFRACTION99.86
1.87-1.920.25721450.22252756X-RAY DIFFRACTION99.97
1.92-1.980.25551430.20832713X-RAY DIFFRACTION99.96
1.98-2.050.2561450.20812749X-RAY DIFFRACTION100
2.05-2.130.25221440.20932749X-RAY DIFFRACTION100
2.14-2.230.2561440.18932724X-RAY DIFFRACTION99.97
2.23-2.350.23031440.19522740X-RAY DIFFRACTION100
2.35-2.50.24951450.20462756X-RAY DIFFRACTION100
2.5-2.690.27471460.21062767X-RAY DIFFRACTION100
2.69-2.960.25261430.21282731X-RAY DIFFRACTION100
2.96-3.390.23671450.19522765X-RAY DIFFRACTION100
3.39-4.270.17881450.16472749X-RAY DIFFRACTION100
4.27-40.290.18431440.17852787X-RAY DIFFRACTION99.76

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