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- PDB-3bsx: Crystal Structure of Human Pumilio 1 in complex with Puf5 RNA -

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Basic information

Entry
Database: PDB / ID: 3bsx
TitleCrystal Structure of Human Pumilio 1 in complex with Puf5 RNA
Components
  • 5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
  • Pumilio homolog 1
KeywordsRNA BINDING PROTEIN/RNA / Protein-RNA Complex / 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 / RNA (> 10) / Pumilio homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 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*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
D: 5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
A: Pumilio homolog 1
B: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)86,5264
Polymers86,5264
Non-polymers00
Water4,432246
1
C: 5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
A: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)43,2632
Polymers43,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-2 kcal/mol
Surface area16950 Å2
MethodPISA
2
D: 5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
B: Pumilio homolog 1


Theoretical massNumber of molelcules
Total (without water)43,2632
Polymers43,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-5.3 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.835, 65.642, 313.975
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*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'


Mass: 3454.066 Da / Num. of mol.: 2 / 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): BL-21 Gold / References: UniProt: Q14671
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, 0.05M Sodium Cacodylate pH 6.5, 0.2M KCl, 0.1M Magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Sodium Cacodylate11
3KCl11
4Magnesium acetate11
5H2O11
6PEG 800012
7Sodium Cacodylate12
8KCl12
9Magnesium acetate12
10H2O12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2007 / Details: Si(111) monochromator
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 33524 / Num. obs: 31513 / % possible obs: 94 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 18.3
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 2788 / Rsym value: 0.164 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M8Y

1m8y


Resolution: 2.32→40.93 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.846 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.672 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27678 3129 10 %RANDOM
Rwork0.21196 ---
obs0.21845 28112 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--2.81 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.32→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 392 0 246 6109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226016
X-RAY DIFFRACTIONr_angle_refined_deg1.5682.0358212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7315679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15924.362282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.466151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5561536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024419
X-RAY DIFFRACTIONr_nbd_refined0.2560.23158
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.213
X-RAY DIFFRACTIONr_mcbond_it1.3011.53510
X-RAY DIFFRACTIONr_mcangle_it1.56725480
X-RAY DIFFRACTIONr_scbond_it3.05632893
X-RAY DIFFRACTIONr_scangle_it4.0774.52732
LS refinement shellResolution: 2.323→2.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 233 -
Rwork0.255 1809 -
obs--83.83 %
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)
10.0997-0.08610.14750.091-0.29321.8646-0.0099-0.03410.0536-0.0427-0.04520.03240.07350.06660.0551-0.0065-0.0150.0028-0.0310.002-0.0028-13.5273-4.013611.0076
20.00010.00190.020.02970.31753.39740.0387-0.06670.0257-0.0398-0.0317-0.0042-0.0634-0.0534-0.007-0.0111-0.05120.09350.068-0.0165-0.0278-12.648920.903566.0852
33.25860.78134.96310.32311.30287.6530.0863-0.4270.0315-0.13710.04840.18340.3851-0.7868-0.13470.0004-0.00270.0302-0.00280.0088-0.0342-21.2856-11.50316.5373
46.18542.71333.85242.43658.134435.72390.2673-0.97790.1458-0.1281-0.0994-0.09291.9927-0.3695-0.167800.00080.00080.00010.0002-0.0003-18.396812.346265.1262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC828 - 11681 - 341
2X-RAY DIFFRACTION2BD828 - 11671 - 340
3X-RAY DIFFRACTION3CA1 - 101 - 10
4X-RAY DIFFRACTION4DB2 - 102 - 10

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