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- PDB-7a1v: Crystal structure of YTHDF2 in complex with m1A -

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Basic information

Entry
Database: PDB / ID: 7a1v
TitleCrystal structure of YTHDF2 in complex with m1A
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
6-AMINO-1-METHYLPURINE / YTH domain-containing family protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 m1A
Authors: Wang, X. / Caflisch, A.
History
DepositionAug 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 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)39,65011
Polymers38,7362
Non-polymers9159
Water1,20767
1
A: YTH domain-containing family protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9026
Polymers19,3681
Non-polymers5345
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)19,7485
Polymers19,3681
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.781, 79.781, 113.563
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-IDDetails
d_1ens_1(chain "A" and (resid 401 through 404 or (resid 405...
d_2ens_1(chain "B" and ((resid 401 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNARGA1 - 111
d_12ens_1ILELYSA113 - 148
d_21ens_1ASNARGC2 - 112
d_22ens_1ILELYSC115 - 150

NCS oper: (Code: givenMatrix: (-0.987130762995, 0.129825632462, 0.0933710978037), (0.125437217629, 0.99076656374, -0.0514501759867), (-0.0991885133613, -0.0390758407626, -0.994301120127)Vector: 79. ...NCS oper: (Code: given
Matrix: (-0.987130762995, 0.129825632462, 0.0933710978037), (0.125437217629, 0.99076656374, -0.0514501759867), (-0.0991885133613, -0.0390758407626, -0.994301120127)
Vector: 79.4553595711, -1.32521817019, 20.2391917476)

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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(DE3) (bacteria) / References: UniProt: Q9Y5A9
#2: Chemical ChemComp-M1A / 6-AMINO-1-METHYLPURINE


Mass: 150.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M Sodium Citrate Tribasic Dihydrate pH 5.2, 2 M ammonium sulfate.
PH range: 4.8-5.4 / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: boiled-off liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→43.87 Å / Num. obs: 40931 / % possible obs: 99.98 % / Redundancy: 7.1 % / Biso Wilson estimate: 49.21 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.041 / Net I/σ(I): 31
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.2-2.333.0165770.8490.64199.4
2.33-2.495.0762140.9410.3971100
2.49-2.698.2557780.9770.2451100
2.69-2.9515.5253630.9930.1251100
2.95-3.332.1448160.9990.061100
3.3-3.857.2942620.9990.0331100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wqn

4wqn


Resolution: 2.2→43.87 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.0249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 1040 5 %
Rwork0.2216 19742 -
obs0.2232 20782 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 52 67 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032479
X-RAY DIFFRACTIONf_angle_d0.48543365
X-RAY DIFFRACTIONf_chiral_restr0.0457347
X-RAY DIFFRACTIONf_plane_restr0.0025430
X-RAY DIFFRACTIONf_dihedral_angle_d17.4317865
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.35571892648 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.34221480.29862797X-RAY DIFFRACTION99.86
2.32-2.460.28731460.27062789X-RAY DIFFRACTION100
2.46-2.650.32571500.27652847X-RAY DIFFRACTION100
2.65-2.920.28561480.27252803X-RAY DIFFRACTION100
2.92-3.340.29611480.24322811X-RAY DIFFRACTION100
3.34-4.210.21311500.19872849X-RAY DIFFRACTION100
4.21-43.870.2341500.19232846X-RAY DIFFRACTION100

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