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- PDB-3bsb: Crystal Structure of Human Pumilio1 in Complex with CyclinB rever... -

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Basic information

Entry
Database: PDB / ID: 3bsb
TitleCrystal Structure of Human Pumilio1 in Complex with CyclinB reverse RNA
Components
  • 5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'
  • Pumilio homolog 1
KeywordsRNA BINDING PROTEIN/RNA / Protein-RNA Complex / Alternative splicing / Cytoplasm / Phosphoprotein / RNA-binding / Translation regulation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGupta, Y.K. / Nair, D.T. / Wharton, R.P. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2008
Title: Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.
Authors: Gupta, Y.K. / Nair, D.T. / Wharton, R.P. / Aggarwal, A.K.
History
DepositionDec 23, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: 5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'
A: Pumilio homolog 1
B: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)82,4143
Polymers82,4143
Non-polymers00
Water2,612145
1
C: 5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'
B: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)42,6052
Polymers42,6052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-8.2 kcal/mol
Surface area16870 Å2
MethodPISA
2
A: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)39,8091
Polymers39,8091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.874, 64.292, 321.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain 5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'


Mass: 2795.655 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Pumilio homolog 1 / Pumilio-1 / HsPUM


Mass: 39808.945 Da / Num. of mol.: 2 / Fragment: Pumilio-Puf domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUM1, KIAA0099, PUMH1 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD / References: UniProt: Q14671
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Hanging drop, pH 6.5, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1H2O11
2H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID10.979
SYNCHROTRONAPS 17-BM20.918
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDAug 4, 2006Mirror
MAR CCD 165 mm2CCDDec 8, 2006Mirror
RadiationMonochromator: cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9181
ReflectionResolution: 2.8→50 Å / Num. obs: 30457 / % possible obs: 92.3 % / Observed criterion σ(F): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.071 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.72 / Num. unique all: 1254 / Rsym value: 0.22 / % possible all: 67.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M8Y

1m8y


Resolution: 2.8→25.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 59076.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2352 7.7 %RANDOM
Rwork0.244 ---
obs0.244 17996 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.9824 Å2 / ksol: 0.304542 e/Å3
Displacement parametersBiso mean: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.32 Å20 Å20 Å2
2--18.28 Å20 Å2
3----12.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 184 0 145 5820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 296 8.3 %
Rwork0.319 3262 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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