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- PDB-7po6: Xist (m6A)UCG tetraloop RNA bound to the YTH domain of YTHDC1 -

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Basic information

Entry
Database: PDB / ID: 7po6
TitleXist (m6A)UCG tetraloop RNA bound to the YTH domain of YTHDC1
Components
  • Isoform 2 of YTH domain-containing protein 1
  • RNA (5'-R(*(6MZ)P*UP*C)-3')
KeywordsRNA BINDING PROTEIN / m6A / YTHDC1 / XIST / Complex
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 / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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 / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJones, A.N. / Mourao, A. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.
Authors: Jones, A.N. / Tikhaia, E. / Mourao, A. / Sattler, M.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA (5'-R(*(6MZ)P*UP*C)-3')
B: Isoform 2 of YTH domain-containing protein 1
A: Isoform 2 of YTH domain-containing protein 1
C: Isoform 2 of YTH domain-containing protein 1
E: RNA (5'-R(*(6MZ)P*UP*C)-3')
F: RNA (5'-R(*(6MZ)P*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,15822
Polymers70,5056
Non-polymers1,65316
Water3,459192
1
D: RNA (5'-R(*(6MZ)P*UP*C)-3')
B: Isoform 2 of YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56110
Polymers23,5022
Non-polymers1,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-30 kcal/mol
Surface area8790 Å2
MethodPISA
2
A: Isoform 2 of YTH domain-containing protein 1
E: RNA (5'-R(*(6MZ)P*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7225
Polymers23,5022
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-5 kcal/mol
Surface area8510 Å2
MethodPISA
3
C: Isoform 2 of YTH domain-containing protein 1
F: RNA (5'-R(*(6MZ)P*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8757
Polymers23,5022
Non-polymers3735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-57 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.438, 85.119, 88.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain / Protein , 2 types, 6 molecules DEFBAC

#1: RNA chain RNA (5'-R(*(6MZ)P*UP*C)-3')


Mass: 4506.766 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Isoform 2 of YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 18994.982 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 208 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris HCl, 0.2M lithium sulfate, 30% (w/v) PEG 4000

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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: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→48.34 Å / Num. obs: 57964 / % possible obs: 98.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.08
Reflection shellResolution: 1.87→2 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 17057 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3I

4r3i


Resolution: 1.77→48.34 Å / SU ML: 0.2945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 2894 4.99 %
Rwork0.2001 55070 -
obs0.2017 57964 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.87 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 205 87 192 4374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124303
X-RAY DIFFRACTIONf_angle_d1.31675848
X-RAY DIFFRACTIONf_chiral_restr0.0628644
X-RAY DIFFRACTIONf_plane_restr0.0093699
X-RAY DIFFRACTIONf_dihedral_angle_d10.9136630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.49631080.4822076X-RAY DIFFRACTION78.96
1.79-1.830.44011230.46952356X-RAY DIFFRACTION89.69
1.83-1.860.46181360.39272593X-RAY DIFFRACTION98.59
1.86-1.890.38071390.34532647X-RAY DIFFRACTION99.89
1.89-1.930.36121380.31042600X-RAY DIFFRACTION99.82
1.93-1.980.27061380.2632648X-RAY DIFFRACTION100
1.98-2.020.3181380.2342617X-RAY DIFFRACTION99.93
2.02-2.070.25811400.21892653X-RAY DIFFRACTION99.96
2.07-2.130.23281380.21652633X-RAY DIFFRACTION99.96
2.13-2.190.24911400.20532641X-RAY DIFFRACTION99.96
2.19-2.260.24071380.21742641X-RAY DIFFRACTION100
2.26-2.340.2551390.18252649X-RAY DIFFRACTION100
2.34-2.440.21481390.18142660X-RAY DIFFRACTION99.93
2.44-2.550.23461400.18892646X-RAY DIFFRACTION100
2.55-2.680.23771400.20392662X-RAY DIFFRACTION99.96
2.68-2.850.29451410.19972674X-RAY DIFFRACTION100
2.85-3.070.25741410.20192681X-RAY DIFFRACTION99.96
3.07-3.380.2161410.18262676X-RAY DIFFRACTION99.96
3.38-3.870.21541440.1772719X-RAY DIFFRACTION100
3.87-4.870.16021420.14622733X-RAY DIFFRACTION99.97
4.87-48.340.20411510.19532865X-RAY DIFFRACTION99.97

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