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- PDB-4rdn: Structure of YTH-YTHDF2 in complex with m6A -

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Basic information

Entry
Database: PDB / ID: 4rdn
TitleStructure of YTH-YTHDF2 in complex with m6A
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / m6A methylated RNA binding / atypical Beta-Propeller / RNA binding / m6A methylated RNA
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
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
N-methyladenosine / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, F.D. / Zhao, D.B. / Wu, J.H. / Shi, Y.Y.
CitationJournal: Cell Res. / Year: 2014
Title: Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition.
Authors: Li, F. / Zhao, D. / Wu, J. / Shi, Y.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)39,6828
Polymers38,7362
Non-polymers9476
Water4,197233
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8414
Polymers19,3681
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8414
Polymers19,3681
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.730, 80.730, 113.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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 / Fragment: UNP residues 408-552
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-6MD / N-methyladenosine


Mass: 281.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 55.37 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Potassium tartrate, 0.1 M Sodium citrate tribasic dehydrate, PH 5.6, 2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→69.914 Å / Num. all: 24524 / Num. obs: 24524 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rsym value: 0.122 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.218.40.5351.42998735770.535100
2.21-2.358.10.4681.42723133580.468100
2.35-2.518.30.3032.52657631830.303100
2.51-2.718.30.24632451729520.246100
2.71-2.978.30.1714.22268927340.171100
2.97-3.328.10.1225.61995824560.122100
3.32-3.837.40.0837.71622621850.083100
3.83-4.78.50.04912.91560618320.049100
4.7-6.648.70.04813.11253414460.048100
6.64-38.0318.40.04411.567488010.04499.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.03 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2484 / WRfactor Rwork: 0.2022 / FOM work R set: 0.8004 / SU B: 5.553 / SU ML: 0.145 / SU R Cruickshank DPI: 0.218 / SU Rfree: 0.1977 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1247 5.1 %RANDOM
Rwork0.2169 ---
obs0.2196 23209 99.87 %-
all-24524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.8 Å2 / Biso mean: 27.687 Å2 / Biso min: 7.18 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 60 233 2709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192553
X-RAY DIFFRACTIONr_bond_other_d0.0010.022353
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9413455
X-RAY DIFFRACTIONr_angle_other_deg0.72535397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1423.516128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31115434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.571518
X-RAY DIFFRACTIONr_chiral_restr0.070.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
X-RAY DIFFRACTIONr_mcbond_it1.1842.6511193
X-RAY DIFFRACTIONr_mcbond_other1.1812.651192
X-RAY DIFFRACTIONr_mcangle_it2.033.9671490
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 94 -
Rwork0.27 1704 -
all-1798 -
obs--99.94 %

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