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- PDB-5kla: Crystal structure of the drosophila Pumilio RNA-binding domain in... -

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Basic information

Entry
Database: PDB / ID: 5kla
TitleCrystal structure of the drosophila Pumilio RNA-binding domain in complex with hunchback RNA
Components
  • Maternal protein pumilio
  • RNA (5'-R(*UP*GP*UP*AP*CP*AP*UP*A)-3')
KeywordsRNA-binding protein/RNA / RNA-binding protein / 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 / : / muscle cell postsynaptic specialization / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / post-transcriptional gene silencing / neuronal ribonucleoprotein granule ...type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / type Ib terminal bouton / head involution / : / muscle cell postsynaptic specialization / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / post-transcriptional gene silencing / neuronal ribonucleoprotein granule / anterior/posterior axis specification, embryo / behavioral response to ethanol / 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 / chemical synaptic transmission / negative regulation of translation / negative regulation of DNA-templated transcription / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Armadillo-like helical ...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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / RNA / Maternal protein pumilio
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: RNA (5'-R(*UP*GP*UP*AP*CP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5417
Polymers41,2402
Non-polymers3015
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint3 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.904, 29.537, 62.034
Angle α, β, γ (deg.)90.000, 101.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1612-

HOH

21A-1856-

HOH

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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: RNA chain RNA (5'-R(*UP*GP*UP*AP*CP*AP*UP*A)-3')


Mass: 2511.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG 3350, 0.1 M bis-tris, pH 6.5 and 0.2 M NH4OAc

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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: 1.14→50 Å / Num. obs: 127177 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.05 / Χ2: 1.033 / Net I/av σ(I): 36.908 / Net I/σ(I): 11.8 / Num. measured all: 531939
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.14-1.162.40.387197.4
1.16-1.183.10.374199.7
1.18-1.23.20.336199.7
1.2-1.233.30.299199.5
1.23-1.253.40.258199.5
1.25-1.283.40.234199.6
1.28-1.323.40.197199.6
1.32-1.353.40.178199.6
1.35-1.393.40.157199.6
1.39-1.443.40.131199.7
1.44-1.493.40.115199.8
1.49-1.553.40.096199.7
1.55-1.623.40.08199.8
1.62-1.73.50.069199.7
1.7-1.813.50.063199.5
1.81-1.956.20.087199.9
1.95-2.1570.0681100
2.15-2.4670.0571100
2.46-3.097.10.0451100
3.09-506.30.036199.8

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Processing

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

3h3d


Resolution: 1.14→34.458 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5
RfactorNum. reflection% reflection
Rfree0.174 12698 9.99 %
Rwork0.1601 --
obs0.1615 127062 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.46 Å2 / Biso mean: 29.1566 Å2 / Biso min: 11.47 Å2
Refinement stepCycle: final / Resolution: 1.14→34.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 166 41 360 3281
Biso mean--47.4 33.53 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073029
X-RAY DIFFRACTIONf_angle_d0.954125
X-RAY DIFFRACTIONf_chiral_restr0.068467
X-RAY DIFFRACTIONf_plane_restr0.006511
X-RAY DIFFRACTIONf_dihedral_angle_d21.0311180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1386-1.15160.26913880.25653559394793
1.1516-1.16510.23934170.237837544171100
1.1651-1.17930.22284240.224238024226100
1.1793-1.19430.23424190.222437634182100
1.1943-1.210.21894180.213837764194100
1.21-1.22660.21574270.20293838426599
1.2266-1.24410.21194190.199337664185100
1.2441-1.26270.21474200.198737814201100
1.2627-1.28240.20284260.19538264252100
1.2824-1.30340.21174150.19437504165100
1.3034-1.32590.21084230.192738084231100
1.3259-1.350.20944250.18738194244100
1.35-1.3760.2054180.18737714189100
1.376-1.40410.20474280.181538594287100
1.4041-1.43460.1934150.177737344149100
1.4346-1.4680.18524270.171638294256100
1.468-1.50470.18114210.165537814202100
1.5047-1.54530.17624290.162738524281100
1.5453-1.59080.17344220.154737914213100
1.5908-1.64220.16434300.15738594289100
1.6422-1.70090.16254200.155137754195100
1.7009-1.7690.17534210.160938254246100
1.769-1.84950.18744250.15833850427599
1.8495-1.9470.17714260.163738404266100
1.947-2.06890.16134260.15683825425199
2.0689-2.22860.16774220.15653830425299
2.2286-2.45290.16274300.15453879430999
2.4529-2.80770.17464300.155838404270100
2.8077-3.53680.17594380.15939324370100
3.5368-34.47340.1594490.145540504499100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17480.59890.1421.7709-0.39191.2576-0.04410.0812-0.06760.0521-0.0715-0.0552-0.0040.22940.10270.1586-0.0092-0.01040.20990.03040.1892-56.6292-0.7804-16.3377
21.26690.96230.28570.5587-0.22951.0255-0.24020.85550.0417-0.17980.216-0.0639-0.02540.2985-0.01220.1768-0.04620.00190.45320.00150.1607-34.95234.3594-14.9912
31.5067-0.09470.5640.5657-0.24721.5513-0.02210.37460.0494-0.0515-0.0117-0.060.00450.31790.01980.152-0.00720.00450.22920.00410.1524-17.84712.71443.9217
41.8682-0.49250.0271.02070.19040.9302-0.0173-0.1603-0.16940.12320.02270.02740.04950.04290.00040.14790.0031-0.0070.11520.00570.1486-18.7565-10.491728.6338
50.072-0.0547-0.21910.1525-0.38750.9781-0.03680.1327-0.0308-0.03710.1790.091-0.036-0.516-0.11190.1641-0.0161-0.00810.23540.01850.169-35.6178-0.849410.3179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1090 through 1137 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1138 through 1232 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1233 through 1315 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1316 through 1426 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 8 )B1 - 8

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