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- PDB-6zd5: Crystal structure of YTHDC1 S378A mutant complex with m6A -

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Basic information

Entry
Database: PDB / ID: 6zd5
TitleCrystal structure of YTHDC1 S378A mutant complex with m6A
ComponentsYTH domain containing 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homologyN-methyladenosine
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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: YTH domain containing 1
B: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13711
Polymers41,9022
Non-polymers1,2359
Water3,297183
1
A: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7137
Polymers20,9511
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4254
Polymers20,9511
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.820, 103.400, 42.490
Angle α, β, γ (deg.)90.000, 105.765, 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 YTH domain containing 1


Mass: 20951.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6MD / N-methyladenosine / N6-Methyladenosine


Mass: 281.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
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: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.89 Å / Num. obs: 14545 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.77
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 2296 / CC1/2: 0.993

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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: 2.3→40.89 Å / SU ML: 0.2654 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 725 5.01 %
Rwork0.186 13757 -
obs0.1883 14482 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 75 183 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782674
X-RAY DIFFRACTIONf_angle_d0.94143631
X-RAY DIFFRACTIONf_chiral_restr0.0504400
X-RAY DIFFRACTIONf_plane_restr0.0054449
X-RAY DIFFRACTIONf_dihedral_angle_d17.8227344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.28741440.20672729X-RAY DIFFRACTION96.96
2.48-2.730.27131450.21722750X-RAY DIFFRACTION99.76
2.73-3.130.27971460.21542767X-RAY DIFFRACTION99.76
3.13-3.940.22671430.18212722X-RAY DIFFRACTION97.75
3.94-40.890.17841470.15372789X-RAY DIFFRACTION99.12

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