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- PDB-5ytx: Crystal structure of YB1 cold-shock domain in complex with UCAACU -

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Basic information

Entry
Database: PDB / ID: 5ytx
TitleCrystal structure of YB1 cold-shock domain in complex with UCAACU
Components
  • Nuclease-sensitive element-binding protein 1
  • RNA (5'-R(P*UP*CP*AP*AP*CP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / YB1 / cold-shock domain / CAAC / 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 / embryonic morphogenesis / histone pre-mRNA 3'end processing complex / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / negative regulation of cellular senescence / epidermis development / mRNA Splicing - Major Pathway / RNA splicing / P-body / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / single-stranded DNA binding / GTPase binding / regulation of gene expression / double-stranded DNA binding / in utero embryonic development / nucleic acid binding / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / synapse / chromatin binding / 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: 1.551 Å
AuthorsYang, X. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China 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: 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
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*UP*CP*AP*AP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)10,8332
Polymers10,8332
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, YB1 can form homodimer in vivo
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint0 kcal/mol
Surface area5140 Å2
Unit cell
Length a, b, c (Å)66.512, 66.512, 33.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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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*UP*CP*AP*AP*CP*U)-3')


Mass: 1836.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
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: BL19U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 12349 / % possible obs: 98.9 % / Redundancy: 6 % / Net I/σ(I): 35.4
Reflection shellResolution: 1.55→1.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PF5

3pf5


Resolution: 1.551→28.801 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.31
RfactorNum. reflection% reflection
Rfree0.2404 1213 9.83 %
Rwork0.2003 --
obs0.2041 12345 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.551→28.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 84 0 50 708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006698
X-RAY DIFFRACTIONf_angle_d0.919962
X-RAY DIFFRACTIONf_dihedral_angle_d11.942271
X-RAY DIFFRACTIONf_chiral_restr0.037114
X-RAY DIFFRACTIONf_plane_restr0.004109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5508-1.61280.36571330.32691213X-RAY DIFFRACTION99
1.6128-1.68620.34161420.30021238X-RAY DIFFRACTION100
1.6862-1.77510.2981350.26051243X-RAY DIFFRACTION100
1.7751-1.88630.2511370.20441207X-RAY DIFFRACTION99
1.8863-2.03190.23431320.19121238X-RAY DIFFRACTION99
2.0319-2.23630.22891310.17451247X-RAY DIFFRACTION99
2.2363-2.55980.21981360.18621253X-RAY DIFFRACTION99
2.5598-3.22440.25381290.20441237X-RAY DIFFRACTION99
3.2244-28.80550.21561380.1831256X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -23.0586 Å / Origin y: -6.8096 Å / Origin z: -35.2714 Å
111213212223313233
T0.1936 Å2-0.0083 Å2-0.0194 Å2-0.1589 Å2-0.0045 Å2--0.1954 Å2
L4.5388 °2-1.5298 °20.0896 °2-5.0538 °2-1.1461 °2--2.6391 °2
S-0.0437 Å °-0.1801 Å °0.2135 Å °0.1607 Å °-0.0346 Å °-0.4653 Å °-0.1685 Å °0.2495 Å °0.0337 Å °
Refinement TLS groupSelection details: all

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