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- PDB-7bik: Crystal structure of YTHDF2 in complex with m6Am -

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Basic information

Entry
Database: PDB / ID: 7bik
TitleCrystal structure of YTHDF2 in complex with m6Am
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / epitranscriptomic 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 / hematopoietic stem cell proliferation / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / negative regulation of Notch signaling pathway / 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 / cell cycle / 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
Chem-TV8 / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of YTHDF2 in complex with m6Am
Authors: Wang, X. / Caflisch, A.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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)39,98013
Polymers38,7362
Non-polymers1,24411
Water2,900161
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9367
Polymers19,3681
Non-polymers5686
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)20,0436
Polymers19,3681
Non-polymers6765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.368, 80.368, 113.769
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1

NCS oper: (Code: givenMatrix: (-0.979623565747, -0.134759397647, -0.148921369116), (-0.140184467419, 0.989770586913, 0.026504723648), (0.143826230321, 0.046841114706, -0.988493766012)Vector: -81. ...NCS oper: (Code: given
Matrix: (-0.979623565747, -0.134759397647, -0.148921369116), (-0.140184467419, 0.989770586913, 0.026504723648), (0.143826230321, 0.046841114706, -0.988493766012)
Vector: -81.5259464034, -8.45372380808, -8.83609329252)

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q9Y5A9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TV8 / (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol


Mass: 295.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2 M ammonium sulphate, 0.1 M Sodium citrate tribasic pH 5.6
Temp details: cold room

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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 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.05 Å / Num. obs: 47916 / % possible obs: 99.98 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 19.73
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
6.24-44.0559.5318140.9990.033199.7
4.44-6.2451.9832460.9990.0381100
3.63-4.4447.4842560.9990.0431100
3.15-3.6334.2549580.9980.061100
2.82-3.1520.0556420.9960.1111100
2.57-2.8211.3262270.9890.2181100
2.38-2.577.4967810.9720.3421100
2.23-2.385.1473170.9290.4871100
2.1-2.233.2476750.8610.743199.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
PHENIX1.19_4080refinement
XDSMarch 15, 2019data reduction
XSCALEMarch 15, 2019data scaling
PHASER1.19_4080phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WQN

4wqn


Resolution: 2.1→44.05 Å / SU ML: 0.2456 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 1215 5 %
Rwork0.1833 23085 -
obs0.1854 24300 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 74 161 2619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742518
X-RAY DIFFRACTIONf_angle_d0.89533407
X-RAY DIFFRACTIONf_chiral_restr0.0602350
X-RAY DIFFRACTIONf_plane_restr0.0044429
X-RAY DIFFRACTIONf_dihedral_angle_d14.1935898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.29611330.22382545X-RAY DIFFRACTION99.96
2.18-2.280.25091360.19412567X-RAY DIFFRACTION99.96
2.28-2.40.26421330.19132543X-RAY DIFFRACTION99.96
2.4-2.550.25331340.19962534X-RAY DIFFRACTION100
2.55-2.750.26331360.22232588X-RAY DIFFRACTION100
2.75-3.030.24181350.19382572X-RAY DIFFRACTION100
3.03-3.470.20351350.18152558X-RAY DIFFRACTION100
3.47-4.370.19991360.15532580X-RAY DIFFRACTION100
4.37-44.050.21421370.17952598X-RAY DIFFRACTION99.96

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