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- PDB-3q0s: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

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Basic information

Entry
Database: PDB / ID: 3q0s
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO2 in complex with erk2 NRE
Components
  • 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'
  • Pumilio homolog 2
KeywordsRNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex
Function / homology
Function and homology information


positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / 3'-UTR-mediated mRNA destabilization / miRNA processing / lncRNA binding ...positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / 3'-UTR-mediated mRNA destabilization / miRNA processing / lncRNA binding / miRNA binding / post-transcriptional regulation of gene expression / hair follicle development / chromosome organization / adipose tissue development / stress granule assembly / regulation of mRNA stability / respiratory electron transport chain / mitochondrion organization / skeletal system development / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / Neddylation / nuclear membrane / neuronal cell body / perinuclear region of cytoplasm / RNA binding / 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
RNA / Pumilio homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLu, G. / Hall, T.M.T.
CitationJournal: Structure / Year: 2011
Title: Alternate modes of cognate RNA recognition by human PUMILIO proteins.
Authors: Lu, G. / Hall, T.M.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pumilio homolog 2
B: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)43,0122
Polymers43,0122
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.404, 45.364, 97.800
Angle α, β, γ (deg.)90.00, 125.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pumilio homolog 2 / Pumilio-2


Mass: 40524.719 Da / Num. of mol.: 1 / Fragment: UNP residues 706-1056
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUM2, KIAA0235, PUMH2 / Plasmid: pDEST527 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8TB72
#2: RNA chain 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Mass: 2487.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA sequence occurs naturally in humans.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 17-20% (w/v) PEG 3000, 100 mM Na3Citrate pH 5.0-6.0 , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 14, 2008
RadiationMonochromator: varimax hf / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24 Å / Num. all: 28271 / Num. obs: 26134 / % possible obs: 92.44 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.4_6)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24 Å / SU ML: 1.18 / σ(F): 0.03 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1279 4.89 %Random
Rwork0.2066 ---
all0.2087 26134 --
obs0.2087 26134 92.44 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.201 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4583 Å20 Å2-2.353 Å2
2--17.6275 Å2-0 Å2
3----16.1692 Å2
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 164 0 136 3083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063019
X-RAY DIFFRACTIONf_angle_d0.8644103
X-RAY DIFFRACTIONf_dihedral_angle_d18.9931171
X-RAY DIFFRACTIONf_chiral_restr0.055463
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.07990.33441220.24662410X-RAY DIFFRACTION81
2.0799-2.17450.26911430.21592733X-RAY DIFFRACTION93
2.1745-2.28910.25591360.19012728X-RAY DIFFRACTION92
2.2891-2.43240.29931340.19312707X-RAY DIFFRACTION91
2.4324-2.61990.27321290.20882688X-RAY DIFFRACTION90
2.6199-2.88320.26331510.20782710X-RAY DIFFRACTION92
2.8832-3.29950.29011440.22222840X-RAY DIFFRACTION95
3.2995-4.15350.20251460.17253014X-RAY DIFFRACTION100
4.1535-24.02710.21931740.19823025X-RAY DIFFRACTION99
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)
10.3840.31040.0660.29450.04860.77810.04240.78880.2871-0.1999-0.17770.0733-0.39530.3645-0.00040.24840.0708-0.00710.57780.07160.30177.216517.87238.6764
21.04620.9638-0.01540.6817-0.12560.81630.05220.6935-0.01080.0230.17890.00710.18030.19220.00010.20960.0527-0.01980.4833-0.04420.2475-0.24178.117110.7421
30.41820.3964-0.63491.0371-1.21571.2736-0.08520.49080.09650.2710.15940.0230.37570.1137-0.00010.29140.1009-0.02310.2567-0.03240.2332-2.2871-1.788616.5247
40.80260.6495-1.00160.5872-0.67011.17510.03380.35630.1002-0.3598-0.03790.16050.520.17490.00010.41080.0571-0.04860.2167-0.01830.2627-5.3735-9.111624.2592
50.50660.0919-0.68780.28220.12720.99360.30440.2222-0.0712-0.1122-0.1860.01880.33810.028400.35120.0475-0.05490.1358-0.02340.2922-8.8725-12.034434.5164
60.5474-0.0685-0.39540.11760.40891.06890.29790.0374-0.14660.1965-0.09690.08440.5944-0.37630.00010.325-0.0477-0.08140.19450.02860.2769-14.4316-11.699743.5233
70.0373-0.0093-0.12180.55530.79960.8940.3024-0.27750.01520.0531-0.08460.09430.1804-0.66060.00010.197-0.0274-0.01810.35740.04030.2509-19.8414-6.79452.5038
80.0655-0.23780.25121.3939-0.20360.72220.5274-0.19740.37940.0918-0.15740.4763-0.2647-1.20250.00020.19190.090.03770.6823-0.03830.4038-25.1102-0.303660.3027
90.9231-0.2929-0.05950.97230.7180.6180.6415-1.26480.07890.4643-0.34920.1619-1.0668-1.67880.02020.43070.30810.10721.0601-0.23380.5242-27.15668.269367.2644
100.3249-0.04420.18750.0424-0.03370.54130.7707-1.18870.45480.130.1386-0.2664-0.8891-2.550.00961.23150.35950.09791.1649-0.19611.0726-24.284718.554366.0835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 706:729)
2X-RAY DIFFRACTION2(chain A and resid 730:766)
3X-RAY DIFFRACTION3(chain A and resid 767:802)
4X-RAY DIFFRACTION4(chain A and resid 803:840)
5X-RAY DIFFRACTION5(chain A and resid 841:876)
6X-RAY DIFFRACTION6(chain A and resid 877:912)
7X-RAY DIFFRACTION7(chain A and resid 913:948)
8X-RAY DIFFRACTION8(chain A and resid 949:984)
9X-RAY DIFFRACTION9(chain A and resid 985:1027)
10X-RAY DIFFRACTION10(chain A and resid 1028:1049)

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