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- PDB-9en7: Hrp48 RRM1 domain -

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Basic information

Entry
Database: PDB / ID: 9en7
TitleHrp48 RRM1 domain
ComponentsHeterogeneous nuclear ribonucleoprotein 27C
KeywordsRNA BINDING PROTEIN / RNA-recognition motif / RRM / translational control
Function / homology
Function and homology information


negative regulation of oskar mRNA translation / pole plasm oskar mRNA localization / poly(G) binding / positive regulation of border follicle cell migration / regulation of mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / P granule / translation repressor activity / positive regulation of translation / mRNA 3'-UTR binding ...negative regulation of oskar mRNA translation / pole plasm oskar mRNA localization / poly(G) binding / positive regulation of border follicle cell migration / regulation of mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / P granule / translation repressor activity / positive regulation of translation / mRNA 3'-UTR binding / mRNA 5'-UTR binding / single-stranded DNA binding / spermatogenesis / ribonucleoprotein complex / mRNA binding / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
DAZ-associated protein 1, RNA recognition motif 2 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein 27C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsLomoschitz, A. / Hennig, J. / Murciano, B. / Meyer, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HE 7291/5-1 Germany
CitationJournal: Biophys.Chem. / Year: 2024
Title: The Drosophila RNA binding protein Hrp48 binds a specific RNA sequence of the msl-2 mRNA 3' UTR to regulate translation.
Authors: Lomoschitz, A. / Meyer, J. / Guitart, T. / Krepl, M. / Lapouge, K. / Hayn, C. / Schweimer, K. / Simon, B. / Sponer, J. / Gebauer, F. / Hennig, J.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein 27C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2863
Polymers10,1021
Non-polymers1842
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint0 kcal/mol
Surface area5580 Å2
Unit cell
Length a, b, c (Å)38.344, 45.496, 57.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein 27C / Hrb27-C / HRP48.1 / hnRNP 48


Mass: 10102.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Hrb27C, hrp48, Rbp7, CG10377 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P48809
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 302 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M K2SO4 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.19→31.82 Å / Num. obs: 32496 / % possible obs: 91.18 % / Redundancy: 12.8 % / Biso Wilson estimate: 14.59 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06499 / Rpim(I) all: 0.01881 / Rrim(I) all: 0.06773 / Net I/σ(I): 18.3
Reflection shellResolution: 1.19→1.233 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 856 / CC1/2: 0.609 / CC star: 0.87 / Rpim(I) all: 0.4347 / Rrim(I) all: 1.597 / % possible all: 26.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootv1.0.0model building
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→31.82 Å / SU ML: 0.0924 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.59
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1703 2000 6.72 %
Rwork0.1625 27742 -
obs0.163 29742 90.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.44 Å2
Refinement stepCycle: LAST / Resolution: 1.19→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms664 0 12 121 797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059696
X-RAY DIFFRACTIONf_angle_d0.8667939
X-RAY DIFFRACTIONf_chiral_restr0.090598
X-RAY DIFFRACTIONf_plane_restr0.0089126
X-RAY DIFFRACTIONf_dihedral_angle_d12.9887259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.220.1749210.226294X-RAY DIFFRACTION13.55
1.22-1.250.2257900.21111256X-RAY DIFFRACTION58.45
1.25-1.290.20441440.22441996X-RAY DIFFRACTION93.16
1.29-1.330.21941570.20452161X-RAY DIFFRACTION98.72
1.33-1.380.18641550.20912160X-RAY DIFFRACTION99.61
1.38-1.430.18921550.1692160X-RAY DIFFRACTION99.7
1.43-1.50.18571570.16032164X-RAY DIFFRACTION99.87
1.5-1.570.15621560.14742172X-RAY DIFFRACTION99.83
1.57-1.670.15061590.15072187X-RAY DIFFRACTION99.91
1.67-1.80.17051570.16292180X-RAY DIFFRACTION99.91
1.8-1.980.17031580.14782202X-RAY DIFFRACTION99.92
1.98-2.270.17071600.15222222X-RAY DIFFRACTION100
2.27-2.860.16971620.16692240X-RAY DIFFRACTION99.88
2.86-31.820.16411690.15982348X-RAY DIFFRACTION99.96

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