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- PDB-7zhh: Complex structure of drosophila Unr CSD789 and a poly(A) RNA sequence -

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Basic information

Entry
Database: PDB / ID: 7zhh
TitleComplex structure of drosophila Unr CSD789 and a poly(A) RNA sequence
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Upstream of N-ras, isoform A
KeywordsRNA BINDING PROTEIN / drosophila Unr / CSD / cold-shock domain / protein-RNA complex
Function / homology
Function and homology information


dosage compensation complex assembly / protein-RNA adaptor activity / RISC complex binding / sex differentiation / lncRNA binding / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cell differentiation / RNA binding / cytosol
Similarity search - Function
: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / 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 / RNA (> 10) / RNA-binding protein Unr
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHollmann, N.M. / Jagtap, P.K.A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
#1: Journal: Nucleic Acids Res. / Year: 2023
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
#2: Journal: Biorxiv / Year: 2022
Title: Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein during translation regulation
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Linse, J.B. / Ullmann, P. / Payr, M. / Murciano, B. / Simon, B. / Hub, J.S. / Hennig, J.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Upstream of N-ras, isoform A
C: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1563
Polymers31,0602
Non-polymers961
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-19 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.920, 36.780, 85.830
Angle α, β, γ (deg.)90.000, 119.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

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Components

#1: Protein Upstream of N-ras, isoform A


Mass: 26166.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, dUnr, dunr, MRE30, UNR, unr, CG7015, Dmel_CG7015
Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VSK3
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 4893.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-Cl (pH 7.0) 0.2 M lithium sulfate 2 M ammonium sulfate

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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: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→48.79 Å / Num. obs: 35311 / % possible obs: 99.5 % / Redundancy: 6.675 % / Biso Wilson estimate: 26.801 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.096 / Χ2: 1.02 / Net I/σ(I): 12.94 / Num. measured all: 235709 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.646.6311.2571.3516691259025170.4921.36497.2
1.64-1.696.6171.0531.6616735253925290.6031.14299.6
1.69-1.736.2340.8552.0115180243724350.6730.93399.9
1.73-1.796.870.6962.6916480240323990.8110.75399.8
1.79-1.856.8930.5053.7215992233223200.890.54699.5
1.85-1.916.7790.3944.7415158224022360.9360.42699.8
1.91-1.986.680.2926.3214388216221540.9610.31699.6
1.98-2.066.2830.2287.6413257211721100.9740.24999.7
2.06-2.166.7810.1810.1813746202820270.9860.195100
2.16-2.266.9320.1511.9613303192419190.9920.16299.7
2.26-2.386.8740.12514.4912538183318240.9920.13599.5
2.38-2.536.7720.11215.911533170717030.9930.12199.8
2.53-2.76.2910.09118.1110280163916340.9940.09999.7
2.7-2.927.040.07622.7610842154515400.9970.08299.7
2.92-3.26.9870.05629.779851141414100.9980.06199.7
3.2-3.586.7090.04536.128507127212680.9980.04999.7
3.58-4.136.1960.03738.556989113911280.9990.04199
4.13-5.066.950.03246.9266099539510.9990.03499.8
5.06-7.156.3880.03440.7249387787730.9990.03799.4
7.15-48.796.2030.0345.4626924444340.9990.03297.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y4H

6y4h


Resolution: 1.6→48.79 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1765 5 %
Rwork0.1872 33543 -
obs0.1884 35308 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.65 Å2 / Biso mean: 25.2251 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.6→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 123 5 266 2081
Biso mean--37.07 35.96 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.40891310.34412482261398
1.64-1.690.31941340.299825562690100
1.69-1.750.33211360.269925802716100
1.75-1.810.26881330.220925382671100
1.81-1.880.24761360.197525662702100
1.88-1.970.21911350.185125652700100
1.97-2.070.24691350.184725712706100
2.07-2.20.18841360.174225882724100
2.2-2.370.22451360.168126002736100
2.37-2.610.22191360.178125922728100
2.61-2.980.20731370.184425902727100
2.98-3.760.16971370.164326152752100
3.76-48.790.18471430.184727002843100

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