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

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Basic information

Entry
Database: PDB / ID: 5bzv
TitleCrystal structure of the RNA-binding domain of yeast Puf5p bound to SMX2 RNA
Components
  • RNA (5'-R(*UP*GP*UP*AP*CP*UP*AP*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


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 / Suppressor protein MPT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.354 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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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*CP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)48,1282
Polymers48,1282
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-6 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.930, 106.930, 167.352
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: uno 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*CP*UP*AP*UP*A)-3')


Mass: 2817.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 15-20% PEG3350, 0.1M CBTP, pH 7.6

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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: 2.35→50 Å / Num. obs: 22619 / % possible obs: 93 % / Redundancy: 7.3 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.8 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BYM

5bym


Resolution: 2.354→45.053 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1999 8.84 %
Rwork0.1883 --
obs0.1923 22610 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.354→45.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 186 0 145 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073191
X-RAY DIFFRACTIONf_angle_d0.9784356
X-RAY DIFFRACTIONf_dihedral_angle_d13.7211214
X-RAY DIFFRACTIONf_chiral_restr0.064534
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3538-2.41270.25141380.19881436X-RAY DIFFRACTION95
2.4127-2.47790.26281430.20421474X-RAY DIFFRACTION96
2.4779-2.55080.23411450.19721483X-RAY DIFFRACTION96
2.5508-2.63310.26431390.19951441X-RAY DIFFRACTION95
2.6331-2.72720.27471420.20471464X-RAY DIFFRACTION95
2.7272-2.83640.28571440.20581478X-RAY DIFFRACTION95
2.8364-2.96550.25851410.21221466X-RAY DIFFRACTION95
2.9655-3.12180.2421420.21231454X-RAY DIFFRACTION94
3.1218-3.31730.2831420.20181476X-RAY DIFFRACTION94
3.3173-3.57330.23711440.19131468X-RAY DIFFRACTION93
3.5733-3.93270.21521410.17381459X-RAY DIFFRACTION93
3.9327-4.50140.23071430.15641476X-RAY DIFFRACTION92
4.5014-5.66950.20391450.17021484X-RAY DIFFRACTION91
5.6695-45.06170.17341500.18961552X-RAY DIFFRACTION89
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)
15.9178-0.837-3.09534.3515-1.52542.54860.22660.81460.0482-0.0468-0.0499-0.0831-0.42680.6438-0.15250.3797-0.01580.00070.66090.03420.22959.029137.8266-33.5985
21.70830.7002-0.03311.4172-0.96346.0044-0.03260.3102-0.0801-0.15280.0130.06450.162-0.18320.01580.15290.01970.02520.2463-0.05330.20143.88129.2679-19.0397
32.79480.0754-0.41154.32081.03734.4193-0.0037-0.1440.22960.06330.1339-0.23530.0790.1816-0.12630.1868-0.00580.06990.2192-0.05530.1694.761330.0186-1.7582
41.43650.41370.11062.72021.60893.3559-0.0711-0.1304-0.09580.41360.06860.05390.29920.14030.020.2549-0.02350.05310.246-0.01160.1814-0.145733.581611.2194
57.63626.58376.43098.4176.95178.8480.0952-0.3893-0.35420.35950.052-0.15420.396-0.2021-0.17140.36810.00150.06510.3782-0.01410.252-5.386937.746126.0854
67.51681.9608-2.91532.1749-0.19563.0276-0.21250.244-0.19760.169-0.01070.48290.1766-0.14010.20950.2937-0.06540.0760.2105-0.06620.2989-10.000546.18723.2135
72.2716-0.23610.74723.11911.6623.2048-0.263-0.3972-0.29050.49230.04250.4821-0.0269-0.04270.15170.47520.00890.15230.27660.00140.3019-10.6849.083930.7901
83.4753-0.4583-0.42921.1399-0.59474.3313-0.3598-0.33710.14810.68440.12360.4115-0.2202-0.12360.17090.53440.03680.14890.2606-0.0910.3438-10.884259.823934.9834
90.0473-0.014-0.60710.0060.17277.79830.02970.09640.1348-0.9540.21570.0968-0.30160.4927-0.68980.637-0.16140.05160.404-0.01480.26765.204549.69652.6953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 234 )
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 322 )
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 425 )
5X-RAY DIFFRACTION5chain 'A' and (resid 426 through 449 )
6X-RAY DIFFRACTION6chain 'A' and (resid 450 through 472 )
7X-RAY DIFFRACTION7chain 'A' and (resid 473 through 556 )
8X-RAY DIFFRACTION8chain 'A' and (resid 557 through 599 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 9 )

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