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- PDB-7f3l: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -

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Basic information

Entry
Database: PDB / ID: 7f3l
TitleCrystal structure of human YBX2 CSD in complex with m5C RNA in space group P62
Components
  • RNA (5'-R(P*CP*AP*UP*(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: 1.88 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 P62
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(P*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)10,7042
Polymers10,7042
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint0 kcal/mol
Surface area5190 Å2
Unit cell
Length a, b, c (Å)67.275, 67.275, 32.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -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: 8876.897 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(P*CP*AP*UP*(5MC))-3')


Mass: 1827.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 2.1 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 PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 6974 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 34.8
Reflection shellResolution: 1.88→1.91 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 365

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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: 6A6L

6a6l


Resolution: 1.88→29.13 Å / SU ML: 0.2119 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 24.4769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 688 10.07 %
Rwork0.1946 6147 -
obs0.1984 6835 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.64 Å2
Refinement stepCycle: LAST / Resolution: 1.88→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms584 83 0 42 709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008684
X-RAY DIFFRACTIONf_angle_d1.2325938
X-RAY DIFFRACTIONf_chiral_restr0.0586108
X-RAY DIFFRACTIONf_plane_restr0.0069109
X-RAY DIFFRACTIONf_dihedral_angle_d20.1066118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.030.28781250.20871131X-RAY DIFFRACTION90.69
2.03-2.230.20381410.18011233X-RAY DIFFRACTION99.85
2.23-2.560.22081340.19951242X-RAY DIFFRACTION99.93
2.56-3.220.24371450.20741256X-RAY DIFFRACTION100
3.22-29.130.22441430.1871285X-RAY DIFFRACTION99.65

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