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- PDB-6zd9: Crystal structure of YTHDC1 apo purified using GST tag -

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Basic information

Entry
Database: PDB / ID: 6zd9
TitleCrystal structure of YTHDC1 apo purified using GST tag
ComponentsYTHDC1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / dosage compensation by inactivation of X chromosome / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBedi, R.K. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
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 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 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 1.3Jan 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
Revision 1.4Oct 1, 2025Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: citation / pdbx_entry_details ...citation / pdbx_entry_details / pdbx_validate_symm_contact / struct_conn
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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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)93,96912
Polymers92,9582
Non-polymers1,01110
Water7,692427
1
A: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7774
Polymers46,4791
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTHDC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1918
Polymers46,4791
Non-polymers7137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.880, 103.980, 41.980
Angle α, β, γ (deg.)90.000, 104.316, 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: 46478.793 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) / References: UniProt: Q96MU7*PLUS
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 45.95 %
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: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→40.68 Å / Num. obs: 51254 / % possible obs: 98.3 % / Redundancy: 3.43 % / Biso Wilson estimate: 19.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.16
Reflection shellResolution: 1.51→1.6 Å / Num. unique obs: 8258 / CC1/2: 0.974

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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: 1.51→40.68 Å / SU ML: 0.1512 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.3021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 2563 5 %
Rwork0.1824 48650 -
obs0.1835 51213 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.14 Å2
Refinement stepCycle: LAST / Resolution: 1.51→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 60 427 3050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542802
X-RAY DIFFRACTIONf_angle_d0.78833809
X-RAY DIFFRACTIONf_chiral_restr0.0539417
X-RAY DIFFRACTIONf_plane_restr0.0045479
X-RAY DIFFRACTIONf_dihedral_angle_d14.6745397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.26031400.23552662X-RAY DIFFRACTION96.55
1.54-1.570.23991430.23092704X-RAY DIFFRACTION99.2
1.57-1.60.27391430.22432717X-RAY DIFFRACTION99.31
1.6-1.640.29611430.21732721X-RAY DIFFRACTION99.34
1.64-1.680.2221440.21472734X-RAY DIFFRACTION98.83
1.68-1.730.26071420.20662691X-RAY DIFFRACTION98.68
1.73-1.780.2561400.21672656X-RAY DIFFRACTION97.9
1.78-1.830.22011390.20942652X-RAY DIFFRACTION95.94
1.83-1.90.24841440.20972734X-RAY DIFFRACTION99.14
1.9-1.980.23961420.20092704X-RAY DIFFRACTION99.51
1.98-2.070.24041430.20112702X-RAY DIFFRACTION99.27
2.07-2.170.21441440.19042747X-RAY DIFFRACTION99.11
2.17-2.310.21221440.18512722X-RAY DIFFRACTION98.73
2.31-2.490.21681420.18312697X-RAY DIFFRACTION97.86
2.49-2.740.19521380.19022627X-RAY DIFFRACTION96.24
2.74-3.140.2021440.18272737X-RAY DIFFRACTION99.04
3.14-3.950.16881450.15642740X-RAY DIFFRACTION99.24
3.95-40.680.1711430.15742703X-RAY DIFFRACTION96.57

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