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- PDB-4rdo: Structure of YTH-YTHDF2 in the free state -

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Basic information

Entry
Database: PDB / ID: 4rdo
TitleStructure of YTH-YTHDF2 in the free state
ComponentsYTH domain-containing family protein 2
KeywordsRNA BINDING PROTEIN / RNA binding / atypical Beta-Propeller / 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 / 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
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
YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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
C: YTH domain-containing family protein 2
D: YTH domain-containing family protein 2
E: YTH domain-containing family protein 2
F: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,78312
Polymers116,2076
Non-polymers5766
Water7,602422
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4642
Polymers19,3681
Non-polymers961
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)19,4642
Polymers19,3681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4642
Polymers19,3681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4642
Polymers19,3681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4642
Polymers19,3681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4642
Polymers19,3681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.280, 139.280, 112.950
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.: 6 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting 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, SITTING 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: Mar 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: 2.15→120.62 Å / Num. all: 65587 / Num. obs: 65587 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.1 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.274.50.5421.44369496980.54298.4
2.27-2.44.50.4051.94133191320.40598.1
2.4-2.574.50.2992.53885585670.29997.9
2.57-2.784.50.2163.53615279690.21697.6
2.78-3.044.50.1255.93309973000.12597.3
3.04-3.44.50.0877.82981365900.08796.9
3.4-3.934.50.0738.42586557680.07396.3
3.93-4.814.30.05411.22039347760.05493.7
4.81-6.84.80.04612.21814437530.04695.1
6.8-42.2764.70.03713.2950220340.03791.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→42.28 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2627 / WRfactor Rwork: 0.2105 / FOM work R set: 0.8152 / SU B: 5.613 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2279 / SU Rfree: 0.2079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 3329 5.1 %RANDOM
Rwork0.2128 ---
obs0.2156 62258 97.01 %-
all-65587 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.8 Å2 / Biso mean: 33.93 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 30 422 7542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197288
X-RAY DIFFRACTIONr_bond_other_d0.0010.026838
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9229829
X-RAY DIFFRACTIONr_angle_other_deg0.737315686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26423.478368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35151287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4571554
X-RAY DIFFRACTIONr_chiral_restr0.080.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021846
X-RAY DIFFRACTIONr_mcbond_it1.8213.1643474
X-RAY DIFFRACTIONr_mcbond_other1.8173.1633473
X-RAY DIFFRACTIONr_mcangle_it2.9054.7334332
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 279 -
Rwork0.253 4607 -
all-4886 -
obs--98.31 %

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