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- PDB-5ytt: Crystal structure of YB1 cold-shock domain in complex with UCAUGU -

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Basic information

Entry
Database: PDB / ID: 5ytt
TitleCrystal structure of YB1 cold-shock domain in complex with UCAUGU
Components
  • Nuclease-sensitive element-binding protein 1
  • RNA (5'-R(P*UP*CP*AP*UP*GP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / YB1 / cold-shock domain / CAUG / 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 / 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 / Interferon gamma signaling / cytoplasmic stress granule / sequence-specific double-stranded DNA binding / single-stranded DNA binding / regulation of gene expression / GTPase binding / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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: 1.6 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: 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*UP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3484
Polymers11,1562
Non-polymers1922
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, YB1 can form homodimer in vivo
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-24 kcal/mol
Surface area5610 Å2
Unit cell
Length a, b, c (Å)66.218, 66.218, 36.080
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*UP*GP*U)-3')


Mass: 2159.299 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
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: 0.97852 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: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 11696 / % possible obs: 96.4 % / Redundancy: 9.2 % / Net I/σ(I): 26.6
Reflection shellResolution: 1.6→1.66 Å

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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: 1.6→30 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.64
RfactorNum. reflection% reflection
Rfree0.2178 1101 10.04 %
Rwork0.1824 --
obs0.1859 10965 46.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 105 30 62 779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007776
X-RAY DIFFRACTIONf_angle_d1.0721082
X-RAY DIFFRACTIONf_dihedral_angle_d14.94304
X-RAY DIFFRACTIONf_chiral_restr0.045131
X-RAY DIFFRACTIONf_plane_restr0.005117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.597-1.66970.2031840.2267759X-RAY DIFFRACTION28
1.6697-1.75770.28811030.196913X-RAY DIFFRACTION35
1.7577-1.86780.19931240.18351073X-RAY DIFFRACTION41
1.8678-2.0120.21261400.1731290X-RAY DIFFRACTION48
2.012-2.21440.17821520.17121356X-RAY DIFFRACTION51
2.2144-2.53470.19191540.17441360X-RAY DIFFRACTION52
2.5347-3.1930.2261620.1981497X-RAY DIFFRACTION56
3.193-30.54410.23711820.17821616X-RAY DIFFRACTION61
Refinement TLS params.Method: refined / Origin x: -6.2485 Å / Origin y: 23.1717 Å / Origin z: 36.1764 Å
111213212223313233
T0.0461 Å2-0.0187 Å20.0274 Å2-0.0806 Å2-0.0269 Å2--0.0923 Å2
L3.1957 °20.3045 °2-0.4893 °2-2.3306 °2-0.36 °2--1.6701 °2
S-0.079 Å °0.0819 Å °-0.314 Å °-0.0379 Å °-0.002 Å °-0.0518 Å °0.2126 Å °-0.096 Å °0.0147 Å °
Refinement TLS groupSelection details: all

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