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- PDB-7f3k: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -

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Basic information

Entry
Database: PDB / ID: 7f3k
TitleCrystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212
Components
  • RNA (5'-R(*UP*CP*AP*UP*(5MC)P*U)-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: 1.76 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 P21212
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(*UP*CP*AP*UP*(5MC)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2254
Polymers12,0332
Non-polymers1922
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area6000 Å2
Unit cell
Length a, b, c (Å)75.749, 33.135, 33.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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.: 1 / 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(*UP*CP*AP*UP*(5MC)P*U)-3')


Mass: 1827.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 3.2 M Ammonium sulfate

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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 PILATUS3 6M / Detector: PIXEL / Date: May 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 8891 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 17.23 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 35.3
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 409

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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: 1.76→33.69 Å / SU ML: 0.1477 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 15.8122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1757 1591 9.82 %
Rwork0.1458 14605 -
obs0.1487 8859 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.32 Å2
Refinement stepCycle: LAST / Resolution: 1.76→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms699 120 10 125 954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065853
X-RAY DIFFRACTIONf_angle_d1.10451179
X-RAY DIFFRACTIONf_chiral_restr0.0513132
X-RAY DIFFRACTIONf_plane_restr0.0055135
X-RAY DIFFRACTIONf_dihedral_angle_d26.9357161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.820.20441510.15281301X-RAY DIFFRACTION98.71
1.82-1.880.19471330.14391336X-RAY DIFFRACTION99.8
1.88-1.960.18771550.1391330X-RAY DIFFRACTION100
1.96-2.050.18131330.14191313X-RAY DIFFRACTION100
2.05-2.160.17941460.13421338X-RAY DIFFRACTION99.93
2.16-2.290.15681490.14721321X-RAY DIFFRACTION100
2.29-2.470.19731470.14851332X-RAY DIFFRACTION100
2.47-2.710.1781390.16931333X-RAY DIFFRACTION100
2.72-3.110.19721450.15271338X-RAY DIFFRACTION100
3.11-3.910.14371410.1361345X-RAY DIFFRACTION100
3.92-33.690.17491520.14341318X-RAY DIFFRACTION99.8

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