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

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Basic information

Entry
Database: PDB / ID: 5bym
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


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 / Suppressor protein MPT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 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 10, 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
C: 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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-7 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.215, 100.792, 49.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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*CP*UP*AP*UP*A)-3')


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 15% PEG3350, 0.1M CTBP

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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 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12843 / % possible obs: 95.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 38
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.2 / % possible all: 73.9

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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

Resolution: 2.708→42.676 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 1279 10 %
Rwork0.2413 --
obs0.2461 12790 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.708→42.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 186 0 0 3111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043179
X-RAY DIFFRACTIONf_angle_d0.7124337
X-RAY DIFFRACTIONf_dihedral_angle_d12.0461209
X-RAY DIFFRACTIONf_chiral_restr0.044531
X-RAY DIFFRACTIONf_plane_restr0.004508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7078-2.81620.38971130.3221020X-RAY DIFFRACTION77
2.8162-2.94430.37931290.31251123X-RAY DIFFRACTION86
2.9443-3.09950.31861360.32281275X-RAY DIFFRACTION97
3.0995-3.29360.38151540.30061306X-RAY DIFFRACTION100
3.2936-3.54780.34971410.27071329X-RAY DIFFRACTION100
3.5478-3.90460.28111490.24161324X-RAY DIFFRACTION100
3.9046-4.46910.25141500.21921348X-RAY DIFFRACTION100
4.4691-5.62850.25341510.2131365X-RAY DIFFRACTION100
5.6285-42.68170.24451560.20581421X-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)
12.01583.61472.65886.45634.75843.5059-0.2090.3207-0.8835-0.251-0.0145-0.7779-0.31640.27380.28980.673-0.15620.00920.7914-0.0131.961546.616640.7519-5.7518
21.92121.948-0.81562.4818-0.47120.58220.2761-0.26291.2639-0.017-0.1350.0088-0.44920.24540.01260.3725-0.19720.07880.2782-0.18222.238736.702539.6905-5.7958
31.75251.149-1.15682.8855-0.00151.0170.0247-0.1810.51440.23350.2212-0.2788-0.02940.2338-0.06450.324-0.0568-0.0390.3775-0.10031.551828.009433.256-3.0164
44.2698-0.5962-2.18860.63150.31282.7218-0.0312-0.3015-0.25520.04070.112-0.24220.0480.2527-0.08030.4088-0.0026-0.11230.4044-0.01341.07911.978728.67456.5809
53.863-0.1347-2.77693.28592.20254.16970.0084-0.5708-0.45430.2241-0.00260.36810.06530.17370.18720.33160.00210.01080.52460.14020.8307-5.911230.367121.6688
65.229-0.7357-0.38052.46051.69143.8516-0.123-0.7554-0.05670.2441-0.06510.6238-0.3112-0.40680.17270.5190.04550.1020.75850.01450.7637-15.812742.205231.0365
79.78461.6827-6.70581.9994-1.43436.01620.2078-0.3981-0.4638-0.22750.4932-1.1294-0.37750.7358-0.65550.8243-0.1336-0.07821.0706-0.26991.141414.985541.17521.741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 202 through 221 )
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 404 )
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 449 )
6X-RAY DIFFRACTION6chain 'A' and (resid 450 through 599 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 9 )

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