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- PDB-5bz5: Crystal structure of the RNA-binding domain of yeast Puf5p bound ... -

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Basic information

Entry
Database: PDB / ID: 5bz5
TitleCrystal structure of the RNA-binding domain of yeast Puf5p bound to AMN1 RNA
Components
  • RNA (5'-R(*UP*GP*UP*AP*AP*CP*UP*UP*UP*A)-3')
  • Suppressor protein MPT5
Keywordsrna binding protein/rna / PUF RNA-binding domain / rna binding protein-rna complex
Function / homology
Function and homology information


positive regulation of mRNA binding / intracellular mRNA localization / regulation of G1 to G0 transition / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / negative regulation of translational initiation / protein-macromolecule adaptor activity / negative regulation of translation / mRNA binding / 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) / Suppressor protein MPT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsQiu, C. / Hall, T.M.T.
CitationJournal: Nat Commun / Year: 2015
Title: RNA regulatory networks diversified through curvature of the PUF protein scaffold.
Authors: Wilinski, D. / Qiu, C. / Lapointe, C.P. / Nevil, M. / Campbell, Z.T. / Tanaka Hall, T.M. / Wickens, M.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor protein MPT5
B: RNA (5'-R(*UP*GP*UP*AP*AP*CP*UP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)49,0472
Polymers49,0472
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-7 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.852, 105.852, 168.404
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Suppressor protein MPT5 / Protein HTR1 / Pumilio homology domain family member 5


Mass: 45310.414 Da / Num. of mol.: 1 / Fragment: unp residues 201-600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MPT5, HTR1, PUF5, YGL178W, BIC834 / Production host: Escherichia coli (E. coli) / References: UniProt: P39016
#2: RNA chain RNA (5'-R(*UP*GP*UP*AP*AP*CP*UP*UP*UP*A)-3')


Mass: 3736.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: PEG3350, CBTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13482 / % possible obs: 93.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.8→38.509 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 1349 10.01 %
Rwork0.2014 --
obs0.2071 13471 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 190 0 13 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033203
X-RAY DIFFRACTIONf_angle_d0.6744371
X-RAY DIFFRACTIONf_dihedral_angle_d12.5631216
X-RAY DIFFRACTIONf_chiral_restr0.046535
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.90010.31961250.27281127X-RAY DIFFRACTION91
2.9001-3.01620.34151340.25571194X-RAY DIFFRACTION94
3.0162-3.15340.28831340.25621203X-RAY DIFFRACTION96
3.1534-3.31960.28641340.23091212X-RAY DIFFRACTION95
3.3196-3.52740.30351340.21311206X-RAY DIFFRACTION95
3.5274-3.79960.25071350.20291216X-RAY DIFFRACTION95
3.7996-4.18150.25851350.17551211X-RAY DIFFRACTION94
4.1815-4.78560.2541350.17181218X-RAY DIFFRACTION94
4.7856-6.02570.24271370.20581238X-RAY DIFFRACTION93
6.0257-38.51240.21221460.18371297X-RAY DIFFRACTION91
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)
13.17420.44040.85423.0356-0.99597.0259-0.00280.7780.0293-0.187-0.14880.0519-0.0430.22050.16340.3220.05930.00910.4462-0.05410.22844.735331.1991-22.9905
21.2548-1.2935-1.66024.1863.13414.6765-0.1671-0.13390.01680.4680.10650.30960.16270.1640.05280.3752-0.05640.03340.37970.00230.2802-5.30341.770720.7505
32.31550.17780.050.863-0.6190.46450.2603-0.3366-0.0997-1.48580.0875-0.0837-1.72721.2461-0.37240.9703-0.14270.09460.7289-0.01570.47664.133749.17583.2072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 203 through 322 )
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 600 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 12 )

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