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- PDB-6ktc: Crystal structure of YBX1 CSD with m5C RNA -

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Basic information

Entry
Database: PDB / ID: 6ktc
TitleCrystal structure of YBX1 CSD with m5C RNA
Components
  • Nuclease-sensitive element-binding protein 1
  • RNA (5'-R(P*GP*(5MC)P*CP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / m5C / CSD / 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: 2.008 Å
AuthorsZou, F. / Li, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.
Authors: Zou, F. / Tu, R. / Duan, B. / Yang, Z. / Ping, Z. / Song, X. / Chen, S. / Price, A. / Li, H. / Scott, A. / Perera, A. / Li, S. / Xie, T.
History
DepositionAug 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
A: Nuclease-sensitive element-binding protein 1
V: RNA (5'-R(P*GP*(5MC)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)9,9422
Polymers9,9422
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-0 kcal/mol
Surface area4950 Å2
Unit cell
Length a, b, c (Å)66.706, 66.706, 34.224
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


Mass: 8710.782 Da / Num. of mol.: 1 / Fragment: CSD domain
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*GP*(5MC)P*CP*U)-3')


Mass: 1230.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 2.5 M Ammonium sulfate, 0.1 M Tris pH 8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 5075 / % possible obs: 97.8 % / Redundancy: 13.2 % / Rsym value: 0.131 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 265 / Rsym value: 0.305 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I2Z

3i2z


Resolution: 2.008→33.353 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.274 222 4.37 %
Rwork0.2371 --
obs0.2388 5075 85.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.008→33.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 84 0 30 683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003668
X-RAY DIFFRACTIONf_angle_d0.647915
X-RAY DIFFRACTIONf_dihedral_angle_d15.754245
X-RAY DIFFRACTIONf_chiral_restr0.022106
X-RAY DIFFRACTIONf_plane_restr0.002105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0079-2.52960.3369860.25672038X-RAY DIFFRACTION73
2.5296-33.35760.25991360.23112815X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.36210.8609-1.26850.7921-0.87871.163-0.1745-0.0476-0.5423-0.03170.24590.3450.2506-0.31380.1330.2306-0.0147-0.02210.18990.01340.30722.118124.91698.6904
23.0205-3.4938-2.58956.45481.82524.02310.1529-0.33850.0955-0.0628-0.2271-0.20320.15980.48920.05790.13660.01850.02030.2230.05980.327410.693322.794311.2681
37.49280.2703-0.18365.87590.19392.26870.1318-0.3603-0.19840.1467-0.09930.201-0.0303-0.0289-0.16620.1316-0.00680.00990.15220.05410.2723.518324.461111.3813
45.7290.3315-1.67165.16053.34034.160.06071.4418-0.0715-1.1983-0.76970.0652-0.3822-0.60570.09590.36430.11310.08450.34930.04180.463710.580226.26580.7191
57.49330.7212-0.53667.31081.60318.32670.0099-0.0355-0.82040.19840.00350.26770.5373-0.1279-0.14050.1550.0413-0.01860.20950.00110.43350.61422.95086.6378
68.35471.00850.15093.65070.31635.0214-0.4429-1.0404-1.2108-0.22090.679-0.90261.07231.5453-0.05730.899-0.0264-0.08420.870.13350.841811.589317.806715.2297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 79 )
6X-RAY DIFFRACTION6chain 'V' and (resid 9 through 12 )

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