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- PDB-6lmr: Solution structure of cold shock domain and ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 6lmr
TitleSolution structure of cold shock domain and ssDNA complex
Components
  • DNA (5'-D(P*AP*AP*CP*AP*CP*CP*T)-3')
  • Y-box-binding protein 1
KeywordsDNA BINDING PROTEIN / Y-box / Cold shock domain / ssNDA / 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 / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / 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 / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / 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 / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / negative regulation of translation / nucleic acid binding / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / 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 (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
DNA / Y-box-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFan, J. / Yang, D.
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 2, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Y-box-binding protein 1
B: DNA (5'-D(P*AP*AP*CP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)13,8792
Polymers13,8792
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1520 Å2
ΔGint14 kcal/mol
Surface area6300 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: 11813.091 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
#2: DNA chain DNA (5'-D(P*AP*AP*CP*AP*CP*CP*T)-3')


Mass: 2066.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D (H)CCH-TOCSY
161isotropic14D NOESY
171isotropic13D filtered NOEST
181isotropic12D 13C/15N filtered TOCSY
191isotropic12D 13C/15N filtered NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] csd, 90% H2O/10% D2O
Label: cn_labeled / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: csd / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 mM / Ionic strength err: 0.5 / Label: con_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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: cyroprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5
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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