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- PDB-6zd8: Crystal structure of YTHDC1 T379V mutant -

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Basic information

Entry
Database: PDB / ID: 6zd8
TitleCrystal structure of YTHDC1 T379V mutant
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBedi, R.K. / Li, Y. / Caflisch, A.
Funding support Switzerland, Sweden, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
Swedish Research CouncilVR 2019-00608 Sweden
CitationJournal: J Chem Theory Comput / Year: 2021
Title: Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1.
Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Sun, X. / Huang, D. / Caflisch, A.
History
DepositionJun 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTHDC1
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,79511
Polymers41,9302
Non-polymers8659
Water7,909439
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3495
Polymers20,9651
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4466
Polymers20,9651
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.760, 103.920, 41.940
Angle α, β, γ (deg.)90.000, 104.671, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein YTHDC1


Mass: 20965.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5

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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: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.57 Å / Num. obs: 52189 / % possible obs: 99.6 % / Redundancy: 3.75 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.02
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8385 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.5→40.57 Å / SU ML: 0.1504 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 2607 5 %
Rwork0.1849 49497 -
obs0.1865 52104 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 45 439 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552715
X-RAY DIFFRACTIONf_angle_d0.78823702
X-RAY DIFFRACTIONf_chiral_restr0.0539400
X-RAY DIFFRACTIONf_plane_restr0.005467
X-RAY DIFFRACTIONf_dihedral_angle_d14.398368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.31721360.26592570X-RAY DIFFRACTION98.58
1.53-1.560.27331360.24872589X-RAY DIFFRACTION99.82
1.56-1.590.29211370.23822603X-RAY DIFFRACTION99.71
1.59-1.630.26071370.23042596X-RAY DIFFRACTION99.78
1.63-1.660.23271380.22152632X-RAY DIFFRACTION99.82
1.66-1.710.25871360.21722583X-RAY DIFFRACTION99.96
1.71-1.750.24731370.21852597X-RAY DIFFRACTION99.24
1.75-1.80.22941360.21442572X-RAY DIFFRACTION98.37
1.8-1.860.22281360.21752585X-RAY DIFFRACTION99.85
1.86-1.930.24021370.20172615X-RAY DIFFRACTION99.89
1.93-20.23161380.19862621X-RAY DIFFRACTION99.75
2-2.10.22251380.18252622X-RAY DIFFRACTION99.96
2.1-2.210.20731380.18662606X-RAY DIFFRACTION99.89
2.21-2.340.25441370.18372606X-RAY DIFFRACTION99.93
2.34-2.530.22381370.18452595X-RAY DIFFRACTION99.78
2.53-2.780.21381370.19072626X-RAY DIFFRACTION99.28
2.78-3.180.21371370.18322599X-RAY DIFFRACTION99.53
3.18-4.010.16181380.15622628X-RAY DIFFRACTION99.75
4.01-40.570.1961410.15892652X-RAY DIFFRACTION99.61

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