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- PDB-5kl1: Crystal structure of the Pumilio-Nos-hunchback RNA complex -

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Basic information

Entry
Database: PDB / ID: 5kl1
TitleCrystal structure of the Pumilio-Nos-hunchback RNA complex
Components
  • Maternal protein pumilio
  • Protein nanos
  • RNA (5'-R(*AP*AP*AP*UP*UP*GP*UP*AP*CP*AP*UP*A)-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 / postsynapse of neuromuscular junction / head involution / 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 / postsynapse of neuromuscular junction / head involution / 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 / sequence-specific mRNA binding / dendrite morphogenesis / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / 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
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: 3.701 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: Derived calculations
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol

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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(*AP*AP*AP*UP*UP*GP*UP*AP*CP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9085
Polymers56,7773
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-22 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.007, 137.007, 221.401
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: 12958.698 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(*AP*AP*AP*UP*UP*GP*UP*AP*CP*AP*UP*A)-3')


Mass: 5090.103 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: 5.28 Å3/Da / Density % sol: 76.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1 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: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 13652 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 140.14 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.042 / Rrim(I) all: 0.135 / Χ2: 0.983 / Net I/av σ(I): 19.114 / Net I/σ(I): 5.2 / Num. measured all: 154091
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.7-3.76110.7471100
3.76-3.8311.20.7261100
3.83-3.9111.50.6891100
3.91-3.9911.60.6431100
3.99-4.0711.70.5251100
4.07-4.1711.90.531100
4.17-4.2711.60.4631100
4.27-4.3911.80.3381100
4.39-4.5211.70.2771100
4.52-4.6611.60.2661100
4.66-4.8311.60.2441100
4.83-5.0211.60.2211100
5.02-5.2511.60.2011100
5.25-5.5311.50.1821100
5.53-5.8711.50.1681100
5.87-6.3211.30.1481100
6.32-6.9611.10.1231100
6.96-7.9610.90.1051100
7.96-10.0210.50.0831100
10.02-509.10.074199.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H3D, 3ALR

3h3d

3alr


Resolution: 3.701→38.325 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.55
RfactorNum. reflection% reflection
Rfree0.3002 1293 9.88 %
Rwork0.2643 --
obs0.2679 13562 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.59 Å2 / Biso mean: 173.681 Å2 / Biso min: 56.83 Å2
Refinement stepCycle: final / Resolution: 3.701→38.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 252 2 0 3446
Biso mean--98.56 --
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033533
X-RAY DIFFRACTIONf_angle_d0.6054824
X-RAY DIFFRACTIONf_chiral_restr0.041550
X-RAY DIFFRACTIONf_plane_restr0.003584
X-RAY DIFFRACTIONf_dihedral_angle_d11.5522131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7011-3.77660.41871270.36621152127988
3.7766-3.85860.36891460.3721288143499
3.8586-3.94830.40621440.34161308145299
3.9483-4.04690.33191500.33211301145199
4.0469-4.15620.42691440.351213171461100
4.1562-4.27840.44241400.339313121452100
4.2784-4.41630.33891470.315513061453100
4.4163-4.57390.3191380.311513381476100
4.5739-4.75670.35561450.324412881433100
4.7567-4.97270.30241470.30112991446100
4.9727-5.23430.30741450.276213191464100
5.2343-5.56130.34761380.284513071445100
5.5613-5.98920.37271460.296813171463100
5.9892-6.58920.29451400.276113191459100
6.5892-7.53640.30291430.265413121455100
7.5364-9.47130.23431380.200113221460100
9.4713-38.3270.22311460.19441304145099

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