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- PDB-3q0r: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

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Basic information

Entry
Database: PDB / ID: 3q0r
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO2 in complex with p38alpha NREb
Components
  • 5'-R(UP*GP*UP*AP*GP*AP*UP*A)-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 / miRNA 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 / miRNA binding / post-transcriptional regulation of gene expression / lncRNA binding / regulation of postsynapse assembly / hair follicle development / adipose tissue development / chromosome organization / regulation of mRNA stability / stress granule assembly / mRNA 3'-UTR binding / skeletal system development / respiratory electron transport chain / mitochondrion organization / cytoplasmic stress granule / regulation of translation / Neddylation / nuclear membrane / postsynapse / neuronal cell body / perinuclear region of cytoplasm / glutamatergic synapse / 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 2
B: 5'-R(UP*GP*UP*AP*GP*AP*UP*A)-3'


Theoretical massNumber of molelcules
Total (without water)43,0762
Polymers43,0762
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-2 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 43.121, 60.612
Angle α, β, γ (deg.)71.93, 85.36, 77.58
Int Tables number1
Space group name H-MP1

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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*GP*AP*UP*A)-3'


Mass: 2551.569 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.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.14 %
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: Mar 17, 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→27.7 Å / Num. all: 23174 / Num. obs: 21575 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 79.8

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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→27.682 Å / SU ML: 0.65 / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 1104 5.12 %Random
Rwork0.2073 ---
all0.2099 21575 --
obs0.2099 21575 93.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.992 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7151 Å2-0.7489 Å2-4.5742 Å2
2---2.6414 Å21.2496 Å2
3---4.3565 Å2
Refinement stepCycle: LAST / Resolution: 2→27.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 169 0 204 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053026
X-RAY DIFFRACTIONf_angle_d1.1224115
X-RAY DIFFRACTIONf_dihedral_angle_d20.3681171
X-RAY DIFFRACTIONf_chiral_restr0.101463
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.09090.29781190.19012264X-RAY DIFFRACTION82
2.0909-2.20110.2781520.19752550X-RAY DIFFRACTION93
2.2011-2.3390.27721300.19442581X-RAY DIFFRACTION94
2.339-2.51950.28351220.2012641X-RAY DIFFRACTION95
2.5195-2.77280.28451530.20422584X-RAY DIFFRACTION95
2.7728-3.17350.2681450.22022641X-RAY DIFFRACTION96
3.1735-3.99640.25661420.19012580X-RAY DIFFRACTION94
3.9964-27.68440.20521410.20352630X-RAY DIFFRACTION96

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