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- PDB-5yts: Crystal structure of YB1 cold-shock domain in complex with UCUUCU -

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Basic information

Entry
Database: PDB / ID: 5yts
TitleCrystal structure of YB1 cold-shock domain in complex with UCUUCU
Components
  • Nuclease-sensitive element-binding protein 1
  • RNA (5'-R(P*CP*UP*UP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / YB1 / cold-shock domain / CUUC / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / positive regulation of cell division / Processing of Capped Intron-Containing Pre-mRNA / epidermis development / mRNA Splicing - Major Pathway / RNA splicing / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / P-body / cytoplasmic stress granule / mRNA processing / Interferon gamma signaling / sequence-specific double-stranded DNA binding / GTPase binding / single-stranded DNA binding / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / nucleic acid binding / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / chromatin binding / synapse / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...: / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / Y-box-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsYang, X. / Huang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China91640102 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010202 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA.
Authors: Yang, X.J. / Zhu, H. / Mu, S.R. / Wei, W.J. / Yuan, X. / Wang, M. / Liu, Y. / Hui, J. / Huang, Y.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclease-sensitive element-binding protein 1
B: RNA (5'-R(P*CP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8833
Polymers10,7872
Non-polymers961
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, YB-1 can form homodimer in vivo
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-16 kcal/mol
Surface area5220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.711, 65.711, 36.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-105-

HOH

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Components

#1: Protein Nuclease-sensitive element-binding protein 1 / CCAAT-binding transcription factor I subunit A / CBF-A / DNA-binding protein B / DBPB / Enhancer ...CCAAT-binding transcription factor I subunit A / CBF-A / DNA-binding protein B / DBPB / Enhancer factor I subunit A / EFI-A / Y-box transcription factor / Y-box-binding protein 1 / YB-1


Mass: 8997.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YBX1, NSEP1, YB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P67809
#2: RNA chain RNA (5'-R(P*CP*UP*UP*C)-3')


Mass: 1790.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.5, 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 16820 / % possible obs: 99 % / Redundancy: 7.3 % / Net I/σ(I): 30.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PF5

3pf5


Resolution: 1.77→30 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.227 886 9.92 %
Rwork0.187 --
obs0.1912 8943 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 80 5 57 716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006706
X-RAY DIFFRACTIONf_angle_d0.901976
X-RAY DIFFRACTIONf_dihedral_angle_d13.751277
X-RAY DIFFRACTIONf_chiral_restr0.036118
X-RAY DIFFRACTIONf_plane_restr0.004111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7695-1.88030.32271400.26871279X-RAY DIFFRACTION96
1.8803-2.02550.26281470.20831320X-RAY DIFFRACTION99
2.0255-2.22930.23141450.1781345X-RAY DIFFRACTION100
2.2293-2.55170.24091500.17821345X-RAY DIFFRACTION100
2.5517-3.21450.23211500.19211358X-RAY DIFFRACTION100
3.2145-32.86110.19851540.1761400X-RAY DIFFRACTION100

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