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- PDB-6nod: Crystal structure of C. elegans PUF-8 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 6nod
TitleCrystal structure of C. elegans PUF-8 in complex with RNA
Components
  • PUF (Pumilio/FBF) domain-containing
  • RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')
Keywordsrna binding protein/rna / PUM repeat protein / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


male meiotic nuclear division / P granule / post-transcriptional regulation of gene expression / negative regulation of MAPK cascade / nuclear periphery / mRNA 3'-UTR binding / regulation of translation / spermatogenesis / cell differentiation / nucleus / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
RNA / PUM-HD domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.547 Å
AuthorsWang, Y. / McCann, K.L. / Qiu, C. / Hall, T.M.T.
CitationJournal: Elife / Year: 2019
Title: Engineering a conserved RNA regulatory protein repurposes its biological function in vivo .
Authors: Bhat, V.D. / McCann, K.L. / Wang, Y. / Fonseca, D.R. / Shukla, T. / Alexander, J.C. / Qiu, C. / Wickens, M. / Lo, T.W. / Tanaka Hall, T.M. / Campbell, Z.T.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUF (Pumilio/FBF) domain-containing
B: PUF (Pumilio/FBF) domain-containing
C: PUF (Pumilio/FBF) domain-containing
D: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')
E: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')
F: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)131,2106
Polymers131,2106
Non-polymers00
Water4,125229
1
A: PUF (Pumilio/FBF) domain-containing
D: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)43,7372
Polymers43,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-3 kcal/mol
Surface area16490 Å2
MethodPISA
2
B: PUF (Pumilio/FBF) domain-containing
E: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)43,7372
Polymers43,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-3 kcal/mol
Surface area16470 Å2
MethodPISA
3
C: PUF (Pumilio/FBF) domain-containing
F: RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)43,7372
Polymers43,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-2 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.182, 189.024, 63.156
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

21B-663-

HOH

31C-667-

HOH

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Components

#1: Protein PUF (Pumilio/FBF) domain-containing / PUF-8


Mass: 41224.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: puf-8, C30G12.7, CELE_C30G12.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09487
#2: RNA chain RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Mass: 2512.529 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3.6 M sodium formate and 10 mM betaine hydrochloride or 3.6 M sodium formate and 3% (w/v) dextran sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.547→50 Å / Num. obs: 39843 / % possible obs: 98.9 % / Redundancy: 6.9 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.547→2.59 Å / Redundancy: 3.6 % / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.547→33.788 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.03
RfactorNum. reflection% reflection
Rfree0.2851 1993 5 %
Rwork0.229 --
obs0.2318 39843 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.547→33.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8415 507 0 229 9151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029147
X-RAY DIFFRACTIONf_angle_d0.4512450
X-RAY DIFFRACTIONf_dihedral_angle_d8.3165529
X-RAY DIFFRACTIONf_chiral_restr0.0371389
X-RAY DIFFRACTIONf_plane_restr0.0031533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5472-2.61080.3451250.25912540X-RAY DIFFRACTION92
2.6108-2.68140.36891380.25432675X-RAY DIFFRACTION98
2.6814-2.76030.30761310.25382718X-RAY DIFFRACTION98
2.7603-2.84930.37531630.26022672X-RAY DIFFRACTION98
2.8493-2.95110.30611550.23392710X-RAY DIFFRACTION99
2.9511-3.06920.27121410.21942692X-RAY DIFFRACTION99
3.0692-3.20880.27791210.22892756X-RAY DIFFRACTION99
3.2088-3.37780.30761500.22692678X-RAY DIFFRACTION99
3.3778-3.58920.3111440.2462683X-RAY DIFFRACTION98
3.5892-3.8660.34031370.27262741X-RAY DIFFRACTION99
3.866-4.25430.27421250.2232724X-RAY DIFFRACTION98
4.2543-4.86840.22461540.19372740X-RAY DIFFRACTION100
4.8684-6.12770.2491550.21442727X-RAY DIFFRACTION100
6.1277-33.79140.22791540.19792794X-RAY DIFFRACTION100

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