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- PDB-6lms: Solution NMR structure cold shock domain of YB1 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 6lms
TitleSolution NMR structure cold shock domain of YB1 from Homo sapiens
ComponentsY-box-binding protein 1
KeywordsTRANSCRIPTION / CSD / DNA binding
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 / mRNA processing / cytoplasmic stress granule / 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, OB-fold
Similarity search - Domain/homology
Y-box-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLi, S. / Zhang, J. / Yang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21735007 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation.
Authors: Zhang, J. / Fan, J.S. / Li, S. / Yang, Y. / Sun, P. / Zhu, Q. / Wang, J. / Jiang, B. / Yang, D. / Liu, M.
History
DepositionDec 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Y-box-binding protein 1


Theoretical massNumber of molelcules
Total (without water)11,6001
Polymers11,6001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5690 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

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


Mass: 11600.004 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 BL21(DE3) (bacteria) / References: UniProt: P67809

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
191isotropic13D HBHA(CO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D (H)CCH-COSY
1121isotropic13D C(CO)NH
1131isotropic23D 1H-13C NOESY aliphatic
1141isotropic23D 1H-13C NOESY aromatic
1151isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] YB1, 90% H2O/10% D2O
Label: 13C, 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: YB1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 0.8 mM, 20 mM PBS, 50 mM NaCl, 1 mM EDTA / Ionic strength: 50 mM / Ionic strength err: 0.2 / Label: conditions_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: eefx force-field
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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