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- PDB-7f3j: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -

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Basic information

Entry
Database: PDB / ID: 7f3j
TitleCrystal structure of human YBX2 CSD in complex with m5C RNA in space group P1
Components
  • RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')
  • Y-box-binding protein 2
KeywordsRNA BINDING PROTEIN/RNA / Complex / protein-RNA / YBX / Cold-shock domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


translational attenuation / oocyte development / positive regulation of cold-induced thermogenesis / spermatogenesis / regulation of gene expression / transcription by RNA polymerase II / nucleic acid binding / DNA binding / RNA binding / nucleus / 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
RNA / Y-box-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, Y. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870741 China
CitationJournal: To Be Published
Title: Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1
Authors: Zhang, Y. / Huang, Y.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Y-box-binding protein 2
B: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')
C: Y-box-binding protein 2
D: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')
E: Y-box-binding protein 2
F: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')
G: Y-box-binding protein 2
H: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)49,3558
Polymers49,3558
Non-polymers00
Water6,269348
1
A: Y-box-binding protein 2
B: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)12,3392
Polymers12,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Y-box-binding protein 2
D: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)12,3392
Polymers12,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Y-box-binding protein 2
F: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)12,3392
Polymers12,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Y-box-binding protein 2
H: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Theoretical massNumber of molelcules
Total (without water)12,3392
Polymers12,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.616, 46.364, 57.704
Angle α, β, γ (deg.)69.264, 85.601, 90.015
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain "A"
21chain "C"
31(chain "E" and resid 89 through 177)
41(chain "G" and resid 89 through 177)
12chain "B"
22chain "D"
32chain "F"
42chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111VALARGA1 - 89
211VALARGC1 - 89
311VALARGE2 - 90
411VALARGG2 - 90
112U5MCB
212U5MCD
312U5MCF
412U5MCH

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999995906075, 0.00152167584034, 0.00242329009791), (0.00152031121656, -0.999998684786, 0.000564871077594), (0.00242414646143, -0.000561184609938, -0.999996904288)21.3277735451, 12.5316264227, -40.9796300425
2given(-0.995560030122, -0.0558468897811, 0.0757717053038), (-0.0898843489063, 0.80303358607, -0.589116171452), (-0.0279469183375, -0.593311203793, -0.804487902463)58.8069800062, 13.0208540916, -32.7675068268
3given(-0.996431279595, -0.0418952634095, 0.0732768172687), (0.0773686972735, -0.800399564299, 0.594453212753), (0.0337459586821, 0.598001107336, 0.800784543993)37.3857088601, 46.1090341077, -8.66309848008
4given(0.999967331644, 0.00488707663411, -0.00643833253235), (0.00500471183317, -0.999818484281, 0.018383453166), (-0.00634732252937, -0.0184150746079, -0.999810280265)21.2234005234, 12.6325195109, -40.5673671104
5given(-0.993713182466, -0.0878350241768, 0.0694198784366), (-0.111948059402, 0.772252034266, -0.625375429296), (0.00132022361063, -0.629215228757, -0.77722998714)59.2048982126, 13.8791573951, -32.6961967045
6given(-0.996129855498, -0.0472435004554, 0.0741172223536), (0.0838381486886, -0.76391663791, 0.639845711987), (0.0263908281259, 0.643583267331, 0.76492097775)37.5045569925, 45.7596913829, -9.55520970893

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Components

#1: Protein
Y-box-binding protein 2 / Contrin / DNA-binding protein C / Dbpc / Germ cell-specific Y-box-binding protein / MSY2 homolog


Mass: 10205.441 Da / Num. of mol.: 4 / Mutation: I92T, Q93K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YBX2, CSDA3, MSY2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2T7
#2: RNA chain
RNA (5'-R(*UP*CP*AP*UP*(5MC))-3')


Mass: 2133.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2020
RadiationMonochromator: 0.97915 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 29797 / % possible obs: 97.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.19 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.276 / Num. unique obs: 1385

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.18.2_3874refinement
Coot0.9.5model building
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6J

6a6j


Resolution: 1.95→24.74 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 23.2506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 1967 7.03 %
Rwork0.1875 26019 -
obs0.1903 27986 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 400 0 348 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733276
X-RAY DIFFRACTIONf_angle_d1.10214510
X-RAY DIFFRACTIONf_chiral_restr0.0628506
X-RAY DIFFRACTIONf_plane_restr0.0065534
X-RAY DIFFRACTIONf_dihedral_angle_d22.0919594
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
1d_2AX-RAY DIFFRACTIONTorsion NCS0.633108553362
1d_3AX-RAY DIFFRACTIONTorsion NCS1.25402830338
1d_4AX-RAY DIFFRACTIONTorsion NCS1.28202662147
2d_2BX-RAY DIFFRACTIONTorsion NCS1.3265448523
2d_3BX-RAY DIFFRACTIONTorsion NCS0.302639545116
2d_4BX-RAY DIFFRACTIONTorsion NCS0.217843723893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.27931180.21471417X-RAY DIFFRACTION70.77
2-2.050.241170.20961496X-RAY DIFFRACTION76.52
2.05-2.110.23061350.19821712X-RAY DIFFRACTION85.59
2.11-2.180.25051340.18851847X-RAY DIFFRACTION93.8
2.18-2.260.22481560.18921948X-RAY DIFFRACTION96.65
2.26-2.350.24671370.19471928X-RAY DIFFRACTION96.99
2.35-2.460.24621490.19121932X-RAY DIFFRACTION96.97
2.46-2.590.29171440.2141944X-RAY DIFFRACTION97.75
2.59-2.750.26771420.21471978X-RAY DIFFRACTION97.92
2.75-2.960.25581510.21291941X-RAY DIFFRACTION98.31
2.96-3.260.25961440.19071966X-RAY DIFFRACTION98.51
3.26-3.730.21271500.1711975X-RAY DIFFRACTION98.79
3.73-4.690.171470.15021966X-RAY DIFFRACTION98.55
4.69-24.740.19621430.18671969X-RAY DIFFRACTION98.65

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