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

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Basic information

Entry
Database: PDB / ID: 5bzu
TitleCrystal structure of the RNA-binding domain of yeast Puf5p bound to AAT2 RNA
Components
  • Suppressor protein MPT5
  • UGUAAUA
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 / RNA (> 10) / Suppressor protein MPT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.501 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: UGUAAUA


Theoretical massNumber of molelcules
Total (without water)48,8042
Polymers48,8042
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-4 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.363, 107.363, 167.226
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 UGUAAUA


Mass: 3493.106 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.: 57 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20049 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2 / % possible all: 96.9

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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: 2.501→32.398 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 1984 9.98 %
Rwork0.2306 --
obs0.2348 19884 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 2.501→32.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 150 0 57 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053147
X-RAY DIFFRACTIONf_angle_d0.8264286
X-RAY DIFFRACTIONf_dihedral_angle_d13.4411188
X-RAY DIFFRACTIONf_chiral_restr0.056523
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5005-2.56310.31551370.2591233X-RAY DIFFRACTION97
2.5631-2.63230.34161370.2771237X-RAY DIFFRACTION97
2.6323-2.70970.36971380.29531239X-RAY DIFFRACTION97
2.7097-2.79720.35261390.2991247X-RAY DIFFRACTION97
2.7972-2.89710.42681380.32071248X-RAY DIFFRACTION97
2.8971-3.0130.40631380.32781241X-RAY DIFFRACTION97
3.013-3.150.3461390.30731262X-RAY DIFFRACTION97
3.15-3.31590.29991410.2651272X-RAY DIFFRACTION99
3.3159-3.52350.28191410.23571274X-RAY DIFFRACTION99
3.5235-3.79510.22181450.2061305X-RAY DIFFRACTION99
3.7951-4.17630.2611400.20641291X-RAY DIFFRACTION98
4.1763-4.7790.21821450.17881283X-RAY DIFFRACTION97
4.779-6.01470.29021480.22321339X-RAY DIFFRACTION99
6.0147-32.40020.19411580.19011429X-RAY DIFFRACTION98
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)
17.2890.4621-2.1886.68610.36328.0348-0.01130.84030.0388-0.29410.00440.23950.9506-1.2976-0.09270.4695-0.0172-0.00360.72-0.04210.3024-8.9853-37.1292-33.5942
21.41240.52110.48052.09110.68647.36980.00840.30760.0764-0.1291-0.0504-0.20480.00030.32670.04550.21610.0586-0.01950.38510.07510.2605-3.8506-29.0991-18.9623
32.51061.8402-2.11913.19021.40526.8458-0.019-0.2204-0.26750.0616-0.02520.08770.0936-0.08090.04080.24450.0181-0.09170.31180.05480.1847-4.7169-30.0782-1.7116
42.32770.14740.93443.5448-1.9364.062-0.0504-0.25670.01390.57060.0974-0.1625-0.2559-0.3883-0.04910.3764-0.0225-0.0730.3384-0.02620.25180.2396-33.689211.1963
56.87314.4866-0.26166.8406-1.48542.30220.3126-0.4844-0.17370.6152-0.1629-0.4677-0.1124-0.0919-0.13450.5881-0.0845-0.13360.30370.01630.30196.9249-41.795524.4914
62.147-0.08990.27351.18790.55340.9671-0.0801-0.24690.29950.63650.0661-0.6594-0.03730.43790.51690.9214-0.1164-0.52220.45690.02110.703415.3083-41.559131.3574
74.8264-1.31470.75750.6226-0.89013.4055-0.1927-0.4116-0.58850.7240.0952-0.66160.46510.19290.11881.0516-0.0806-0.37570.40450.15320.692210.0258-57.571433.0236
81.1767-1.95892.34023.2724-3.80795.42430.32180.1515-0.0491-1.2017-0.15020.07212.0048-0.2666-0.31750.9378-0.2112-0.09690.6594-0.02120.5701-4.3036-50.90184.4116
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 470 )
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 507 )
7X-RAY DIFFRACTION7chain 'A' and (resid 508 through 599 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 11 )

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