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- PDB-7f3i: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -

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Basic information

Entry
Database: PDB / ID: 7f3i
TitleCrystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121
Components
  • RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')
  • Y-box-binding protein 2
KeywordsRNA BINDING PROTEIN/RNA / Complex / protein-RNA / YBX / Cold-shock domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


translational attenuation / oocyte development / positive regulation of cold-induced thermogenesis / spermatogenesis / regulation of gene expression / transcription by RNA polymerase II / nucleic acid binding / DNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / Y-box-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhang, Y. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870741 China
CitationJournal: To Be Published
Title: Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121
Authors: Zhang, Y. / Huang, Y.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Y-box-binding protein 2
B: RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')
C: Y-box-binding protein 2
D: RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')
E: Y-box-binding protein 2


Theoretical massNumber of molelcules
Total (without water)33,7185
Polymers33,7185
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.532, 59.348, 118.623
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
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.829342431012, -0.501436943612, 0.246479458991), (-0.558676780451, 0.73753035992, -0.379380051112), (0.00844908919487, -0.452338324463, -0.891806398897)-40.4921699552, 16.6770088796, 33.1716107333
2given(-0.755747113564, -0.653824208135, -0.0368809598105), (0.43613708919, -0.460515289062, -0.773117137291), (0.488498454217, -0.600366199413, 0.633190087438)-24.2695677006, -5.37384369274, -6.88916284473

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Components

#1: Protein Y-box-binding protein 2 / Contrin / DNA-binding protein C / Dbpc / Germ cell-specific Y-box-binding protein / MSY2 homolog


Mass: 10205.441 Da / Num. of mol.: 3 / Mutation: I92T, Q93K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YBX2, CSDA3, MSY2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2T7
#2: RNA chain RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')


Mass: 1550.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Imidazole, 20% (w/v) PEG 8000, 3% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 15180 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 29.94 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 18.2
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.477 / Num. unique obs: 757

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6J

6a6j


Resolution: 2.25→29.67 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.3658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 1500 10 %
Rwork0.1849 13499 -
obs0.1909 14999 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.28 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 204 0 142 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092402
X-RAY DIFFRACTIONf_angle_d1.26993290
X-RAY DIFFRACTIONf_chiral_restr0.0622361
X-RAY DIFFRACTIONf_plane_restr0.0061405
X-RAY DIFFRACTIONf_dihedral_angle_d27.2036389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.25191250.18991125X-RAY DIFFRACTION92.52
2.33-2.410.2991330.19121190X-RAY DIFFRACTION98.07
2.41-2.50.2891320.20651195X-RAY DIFFRACTION99.1
2.51-2.620.29611340.21251210X-RAY DIFFRACTION99.26
2.62-2.760.29961370.20631229X-RAY DIFFRACTION99.85
2.76-2.930.28611370.19751230X-RAY DIFFRACTION99.93
2.93-3.160.24291360.19981229X-RAY DIFFRACTION100
3.16-3.470.24691360.17341225X-RAY DIFFRACTION99.93
3.47-3.970.22141400.17341263X-RAY DIFFRACTION100
3.97-50.19231410.15311261X-RAY DIFFRACTION100
5-29.670.24891490.19951342X-RAY DIFFRACTION99.93

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