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- PDB-3q0n: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

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Basic information

Entry
Database: PDB / ID: 3q0n
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO1 in complex with erk2 NRE
Components
  • 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'
  • Pumilio homolog 1
KeywordsRNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis ...regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis / mRNA destabilization / regulation of mRNA stability / adult locomotory behavior / mRNA 3'-UTR binding / stem cell differentiation / P-body / cytoplasmic stress granule / regulation of translation / spermatogenesis / regulation of cell cycle / axon / RNA binding / nucleoplasm / cytosol / cytoplasm
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pumilio homolog 1
B: Pumilio homolog 1
C: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'
D: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)85,7044
Polymers85,7044
Non-polymers00
Water4,107228
1
A: Pumilio homolog 1
C: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)42,8522
Polymers42,8522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-6 kcal/mol
Surface area16670 Å2
MethodPISA
2
B: Pumilio homolog 1
D: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)42,8522
Polymers42,8522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-3 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.672, 37.677, 82.551
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pumilio homolog 1 / HsPUM / Pumilio-1


Mass: 40364.523 Da / Num. of mol.: 2 / Fragment: UNP residues 828-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUM1, KIAA0099, PUMH1 / Plasmid: pTYB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14671
#2: RNA chain 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Mass: 2487.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This RNA sequence occurs naturally in humans.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 15-20% (w/v) PEG 3350, 100 mM Li2SO4, and 100 mM Na3Citrate pH 5.5-6.0 , 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: Jul 5, 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: 2.4→22.9 Å / Num. all: 31558 / Num. obs: 31306 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 94.2

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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: 2.4→22.886 Å / SU ML: 1.07 / σ(F): 1.89 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1583 5.06 %Random
Rwork0.2022 ---
all0.2052 31306 --
obs0.2052 31306 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.86 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5432 Å20 Å2-0.08 Å2
2--7.4967 Å2-0 Å2
3---2.0465 Å2
Refinement stepCycle: LAST / Resolution: 2.4→22.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 308 0 228 6026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055945
X-RAY DIFFRACTIONf_angle_d0.8648094
X-RAY DIFFRACTIONf_dihedral_angle_d18.7962279
X-RAY DIFFRACTIONf_chiral_restr0.059913
X-RAY DIFFRACTIONf_plane_restr0.0031003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48360.30571250.22472792X-RAY DIFFRACTION93
2.4836-2.58290.35161620.22312952X-RAY DIFFRACTION100
2.5829-2.70030.30471790.21732948X-RAY DIFFRACTION100
2.7003-2.84240.31691460.21542954X-RAY DIFFRACTION100
2.8424-3.02010.31981630.22222960X-RAY DIFFRACTION100
3.0201-3.25270.26781320.20593007X-RAY DIFFRACTION100
3.2527-3.57890.22831620.18412982X-RAY DIFFRACTION100
3.5789-4.09420.21071550.16843007X-RAY DIFFRACTION100
4.0942-5.14860.22541620.17233004X-RAY DIFFRACTION99
5.1486-22.88670.24281970.21083117X-RAY DIFFRACTION100

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