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- PDB-6sz8: Crystal structure of YTHDC1 with fragment 6 (DHU_DC1_034) -

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Basic information

Entry
Database: PDB / ID: 6sz8
TitleCrystal structure of YTHDC1 with fragment 6 (DHU_DC1_034)
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / Fragment / Complex / YTHDC1 / Epitranscriptomic
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
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
6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione / YTH domain-containing family protein / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsBedi, R.K. / Huang, D. / Sledz, P. / Caflisch, A.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments.
Authors: Bedi, R.K. / Huang, D. / Wiedmer, L. / Li, Y. / Dolbois, A. / Wojdyla, J.A. / Sharpe, M.E. / Caflisch, A. / Sledz, P.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Sep 29, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_src_gen / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly / pdbx_validate_symm_contact / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.1Jan 24, 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 protein 1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5968
Polymers41,9342
Non-polymers6626
Water7,044391
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1593
Polymers20,9671
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4375
Polymers20,9671
Non-polymers4694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.858, 103.913, 42.194
Angle α, β, γ (deg.)90.000, 104.175, 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 protein 1 / Splicing factor YT521 / YT521-B


Mass: 20967.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7, UniProt: A0A2K6KCS5*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-M1Z / 6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione


Mass: 181.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
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: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→40.92 Å / Num. obs: 54009 / % possible obs: 94.9 % / Redundancy: 3.06 % / Biso Wilson estimate: 21.9 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.22
Reflection shellResolution: 1.46→1.55 Å / Num. unique obs: 8272 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 1.47→40.91 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.7601
RfactorNum. reflection% reflection
Rfree0.2494 1996 3.7 %
Rwork0.2161 --
obs0.2174 53944 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.47→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 38 391 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622605
X-RAY DIFFRACTIONf_angle_d0.81413527
X-RAY DIFFRACTIONf_chiral_restr0.0825385
X-RAY DIFFRACTIONf_plane_restr0.0052440
X-RAY DIFFRACTIONf_dihedral_angle_d9.69471521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.36881130.36363129X-RAY DIFFRACTION79.71
1.5-1.540.35281440.33933814X-RAY DIFFRACTION98.02
1.54-1.590.39491460.31573846X-RAY DIFFRACTION98.69
1.59-1.640.32071530.29183787X-RAY DIFFRACTION97.79
1.64-1.70.31181460.28893815X-RAY DIFFRACTION97.51
1.7-1.770.28931450.29123743X-RAY DIFFRACTION96.38
1.77-1.850.35451340.27933667X-RAY DIFFRACTION93.92
1.85-1.950.29471480.28063697X-RAY DIFFRACTION94.45
1.95-2.070.26861390.25263713X-RAY DIFFRACTION95.11
2.07-2.230.29631400.23533699X-RAY DIFFRACTION93.89
2.23-2.450.23021480.21883603X-RAY DIFFRACTION93.45
2.45-2.810.27071480.2163684X-RAY DIFFRACTION93.37
2.81-3.530.20891450.18863854X-RAY DIFFRACTION98.33
3.53-40.910.20031470.16423897X-RAY DIFFRACTION98.2

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