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- PDB-5kl8: Crystal structure of the Pumilio-Nos-CyclinB RNA complex -

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Basic information

Entry
Database: PDB / ID: 5kl8
TitleCrystal structure of the Pumilio-Nos-CyclinB RNA complex
Components
  • Maternal protein pumilio
  • Protein nanos
  • RNA (5'-R(*UP*AP*UP*UP*UP*GP*UP*AP*AP*UP*U)-3')
KeywordsRNA-binding protein/RNA / RNA-binding proteins / RNA-binding protein-RNA complex
Function / homology
Function and homology information


type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / type Ib terminal bouton / head involution / postsynapse of neuromuscular junction / negative regulation of synaptic assembly at neuromuscular junction / : / oocyte anterior/posterior axis specification / pole plasm / muscle cell postsynaptic specialization ...type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / type Ib terminal bouton / head involution / postsynapse of neuromuscular junction / negative regulation of synaptic assembly at neuromuscular junction / : / oocyte anterior/posterior axis specification / pole plasm / muscle cell postsynaptic specialization / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / segmentation / : / post-transcriptional gene silencing / neuronal ribonucleoprotein granule / anterior/posterior axis specification, embryo / germ-line stem cell population maintenance / behavioral response to ethanol / germ cell migration / miRNA processing / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / dendrite morphogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / : / oogenesis / negative regulation of epidermal growth factor receptor signaling pathway / germ cell development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cell cycle / long-term memory / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / modulation of chemical synaptic transmission / neuromuscular junction / cell migration / nuclear envelope / mitotic cell cycle / postsynapse / spermatogenesis / chemical synaptic transmission / negative regulation of translation / negative regulation of DNA-templated transcription / mRNA binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nanos, RNA-binding domain / Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / HIV-1 Nucleocapsid Protein / Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. ...Nanos, RNA-binding domain / Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / HIV-1 Nucleocapsid Protein / Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Few Secondary Structures / Irregular / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein nanos / Maternal protein pumilio
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsQiu, C. / Hall, T.M.T.
CitationJournal: Elife / Year: 2016
Title: Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio.
Authors: Weidmann, C.A. / Qiu, C. / Arvola, R.M. / Lou, T.F. / Killingsworth, J. / Campbell, Z.T. / Tanaka Hall, T.M. / Goldstrohm, A.C.
History
DepositionJun 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maternal protein pumilio
B: Protein nanos
C: RNA (5'-R(*UP*AP*UP*UP*UP*GP*UP*AP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2905
Polymers56,1593
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.102, 135.102, 220.402
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Maternal protein pumilio


Mass: 38728.398 Da / Num. of mol.: 1 / Fragment: UNP residues 1091-1426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pum, CG9755 / Production host: Escherichia coli (E. coli) / References: UniProt: P25822
#2: Protein Protein nanos


Mass: 13057.830 Da / Num. of mol.: 1 / Fragment: UNP residues 289-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nos, CG5637 / Production host: Escherichia coli (E. coli) / References: UniProt: P25724
#3: RNA chain RNA (5'-R(*UP*AP*UP*UP*UP*GP*UP*AP*AP*UP*U)-3')


Mass: 4372.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 5.17 Å3/Da / Density % sol: 76.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.9 M ammonium sulfate, 0.1 M MES, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.992 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 10740 / % possible obs: 99.3 % / Redundancy: 8.9 % / Biso Wilson estimate: 182.06 Å2 / Rmerge(I) obs: 0.143 / Net I/av σ(I): 12.987 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
4-4.078.70.7791100
4.07-4.148.80.731100
4.14-4.228.80.7171100
4.22-4.318.90.5871100
4.31-4.490.4921100
4.4-4.59.10.4011100
4.5-4.629.20.3581100
4.62-4.749.40.3621100
4.74-4.889.50.2991100
4.88-5.049.50.2851100
5.04-5.229.50.2561100
5.22-5.439.50.2511100
5.43-5.679.40.229199.8
5.67-5.979.40.187199.6
5.97-6.359.30.157199.5
6.35-6.849.10.131199.6
6.84-7.5290.119199.5
7.52-8.68.40.106198.9
8.6-10.827.70.111199.1
10.82-505.80.101192.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→39.001 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.07
RfactorNum. reflection% reflection
Rfree0.3119 1073 10.01 %
Rwork0.2829 --
obs0.2863 10715 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 354.67 Å2 / Biso mean: 206.8689 Å2 / Biso min: 99.36 Å2
Refinement stepCycle: final / Resolution: 4→39.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 226 2 0 3247
Biso mean--111.94 --
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023323
X-RAY DIFFRACTIONf_angle_d0.5084530
X-RAY DIFFRACTIONf_chiral_restr0.038520
X-RAY DIFFRACTIONf_plane_restr0.003549
X-RAY DIFFRACTIONf_dihedral_angle_d11.6442011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9772-4.1580.36631300.373411631293100
4.158-4.37690.3951300.358611771307100
4.3769-4.65070.33721310.345511811312100
4.6507-5.00910.34911330.322311931326100
5.0091-5.5120.34161320.315911901322100
5.512-6.30670.33141350.318712181353100
6.3067-7.93470.35611370.304812311368100
7.9347-39.00240.26151450.22471289143497

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