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- PDB-3q0p: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

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Basic information

Entry
Database: PDB / ID: 3q0p
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO1 in complex with hunchback NRE
Components
  • 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-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: 2.6 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,8256
Polymers85,7544
Non-polymers712
Water2,486138
1
A: Pumilio homolog 1
C: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9133
Polymers42,8772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-7 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: Pumilio homolog 1
D: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9133
Polymers42,8772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.326, 37.483, 82.299
Angle α, β, γ (deg.)90.00, 102.83, 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*UP*AP*UP*A)-3'


Mass: 2512.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This RNA occurs in flies.
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
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: Aug 24, 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: 2.6→23.8 Å / Num. all: 24731 / Num. obs: 22777 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 95.1

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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: 2.6→23.786 Å / SU ML: 2.04 / σ(F): 0.06 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 1148 5.04 %Random
Rwork0.193 ---
all0.1965 22777 --
obs0.1965 22777 92.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.714 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3698 Å20 Å2-0.3117 Å2
2--3.1271 Å2-0 Å2
3---1.2427 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 332 2 138 5962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055973
X-RAY DIFFRACTIONf_angle_d0.9028138
X-RAY DIFFRACTIONf_dihedral_angle_d19.152293
X-RAY DIFFRACTIONf_chiral_restr0.06918
X-RAY DIFFRACTIONf_plane_restr0.0031004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71760.31231420.21062441X-RAY DIFFRACTION84
2.7176-2.86070.33861250.21822486X-RAY DIFFRACTION86
2.8607-3.03960.29931300.22192534X-RAY DIFFRACTION87
3.0396-3.27370.30841240.21482705X-RAY DIFFRACTION93
3.2737-3.60210.26271440.18612831X-RAY DIFFRACTION96
3.6021-4.1210.25541560.1672827X-RAY DIFFRACTION96
4.121-5.18320.21691430.15822836X-RAY DIFFRACTION96
5.1832-23.78680.23161840.1942969X-RAY DIFFRACTION98

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