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- PDB-6a6l: Crystal structure of the cold shock domain of YB-1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6a6l
TitleCrystal structure of the cold shock domain of YB-1 in complex with m5C RNA
Components
  • Nuclease-sensitive element-binding protein 1
  • RNA (5'-R(P*CP*AP*UP*(5MC))-3')
KeywordsRNA BINDING PROTEIN/RNA / CSD domain / CAUC motif / 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 / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHuang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China91640102 China
Chinese Academy of SciencesXDB08010202 China
CitationJournal: To Be Published
Title: Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA
Authors: Huang, Y.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Nuclease-sensitive element-binding protein 1
D: RNA (5'-R(P*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)10,8242
Polymers10,8242
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-0 kcal/mol
Surface area5180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.380, 66.380, 34.702
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
11D-104-

HOH

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Components

#1: Protein Nuclease-sensitive element-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: YB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P67809
#2: RNA chain RNA (5'-R(P*CP*AP*UP*(5MC))-3')


Mass: 1827.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 8518 / % possible obs: 100 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 67.973
Reflection shellResolution: 1.78→1.84 Å / Rmerge(I) obs: 0.191 / Num. unique obs: 856

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PF5

3pf5


Resolution: 1.78→29.709 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 21.67
RfactorNum. reflection% reflection
Rfree0.2068 857 10.08 %
Rwork0.1798 --
obs0.1826 8504 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 83 0 58 724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006684
X-RAY DIFFRACTIONf_angle_d0.934940
X-RAY DIFFRACTIONf_dihedral_angle_d12.467256
X-RAY DIFFRACTIONf_chiral_restr0.037109
X-RAY DIFFRACTIONf_plane_restr0.004108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7803-1.89180.26241410.17151257X-RAY DIFFRACTION100
1.8918-2.03790.23231420.17521262X-RAY DIFFRACTION100
2.0379-2.24290.19621400.16761261X-RAY DIFFRACTION100
2.2429-2.56730.20691460.1731271X-RAY DIFFRACTION100
2.5673-3.23390.18681420.19341272X-RAY DIFFRACTION100
3.2339-29.71290.20831460.1811324X-RAY DIFFRACTION100

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