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- PDB-5bz1: Crystal structure of the RNA-binding domain of yeast Puf5p bound ... -

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Basic information

Entry
Database: PDB / ID: 5bz1
TitleCrystal structure of the RNA-binding domain of yeast Puf5p bound to MFA2 RNA
Components
  • RNA (5'-R(*UP*GP*UP*AP*UP*UP*UP*GP*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: 2.15 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*UP*UP*UP*GP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)48,4512
Polymers48,4512
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.748, 106.748, 167.678
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*UP*UP*UP*GP*UP*A)-3')


Mass: 3140.860 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.: 208 / 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: 56.78 %
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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 31214 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 22.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.2 / % possible all: 94.6

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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: 2.15→40.479 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1999 6.41 %
Rwork0.1786 --
obs0.1807 31174 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→40.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 207 0 208 3402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043296
X-RAY DIFFRACTIONf_angle_d0.7874513
X-RAY DIFFRACTIONf_dihedral_angle_d13.031259
X-RAY DIFFRACTIONf_chiral_restr0.051552
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20380.28411330.2381926X-RAY DIFFRACTION95
2.2038-2.26340.2821370.21112012X-RAY DIFFRACTION98
2.2634-2.330.25631420.20632059X-RAY DIFFRACTION100
2.33-2.40520.23171380.19292036X-RAY DIFFRACTION100
2.4052-2.49110.25181410.18572063X-RAY DIFFRACTION100
2.4911-2.59090.21861420.19412068X-RAY DIFFRACTION100
2.5909-2.70880.23171420.18782069X-RAY DIFFRACTION100
2.7088-2.85150.2451420.18682075X-RAY DIFFRACTION100
2.8515-3.03010.22791430.19432087X-RAY DIFFRACTION100
3.0301-3.2640.20261430.19442093X-RAY DIFFRACTION100
3.264-3.59230.19941450.17932106X-RAY DIFFRACTION100
3.5923-4.11170.21131470.15952140X-RAY DIFFRACTION100
4.1117-5.17860.17791470.14282148X-RAY DIFFRACTION100
5.1786-40.48590.17461570.17942293X-RAY DIFFRACTION99
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)
13.7841-1.2313-1.02922.95680.68935.47170.09590.72410.0001-0.4066-0.08460.00380.327-0.3374-0.00590.2828-0.0133-0.02350.4360.03340.222499.1618-33.6307135.8224
21.56590.63160.25091.99620.86244.40170.05710.15-0.0429-0.1233-0.0596-0.1033-0.09470.22990.00250.21620.0329-0.04880.31360.06360.2416103.199-29.3714152.0385
30.7459-0.140.43022.2548-1.99614.3653-0.0735-0.08940.1030.28630.0654-0.0422-0.2957-0.15380.00760.2006-0.0076-0.04060.21620.01670.1956105.1785-32.4544174.8497
45.06666.4824-4.78098.5323-5.72915.24450.2296-0.61150.52450.6577-0.12640.2654-0.3850.2018-0.16170.32030.0119-0.06210.37180.00120.3088111.953-37.8293193.6349
59.20343.05954.90044.20440.1135.8594-0.28790.5868-0.1009-0.0190.014-0.7015-0.15510.35240.24580.2735-0.0387-0.03510.21780.07740.285117.3081-46.4044190.7314
63.11730.1723-0.26995.6506-0.95043.0228-0.2897-0.41820.310.44720.0468-0.7229-0.15760.20.18890.46820.01-0.17490.29620.01280.3085118.0754-48.7398198.0387
74.96344.3884-1.72818.1732-0.73698.56480.1136-0.9122-0.24320.9602-0.5314-1.0452-0.34050.86720.40560.47890.1077-0.21640.36150.06710.4837120.5783-54.0803205.8263
82.92381.51764.01323.82111.35425.67970.3975-0.2086-0.83190.066-0.0581-0.18190.4518-0.2816-0.26910.491-0.0005-0.05980.29780.07830.3332116.0724-64.7412198.6182
90.6976-0.1431-0.19762.2836-1.24780.78130.34810.1701-0.0116-0.5949-0.1320.20490.7830.2329-0.26550.48610.0094-0.0650.3160.00850.3099100.7826-50.3571167.3558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 203 through 257 )
2X-RAY DIFFRACTION2chain 'A' and (resid 258 through 321 )
3X-RAY DIFFRACTION3chain 'A' and (resid 322 through 425 )
4X-RAY DIFFRACTION4chain 'A' and (resid 426 through 449 )
5X-RAY DIFFRACTION5chain 'A' and (resid 450 through 473 )
6X-RAY DIFFRACTION6chain 'A' and (resid 474 through 553 )
7X-RAY DIFFRACTION7chain 'A' and (resid 554 through 579 )
8X-RAY DIFFRACTION8chain 'A' and (resid 580 through 599 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 10 )

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