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- PDB-6ny5: Crystal structure of the PUM-HD domain of S. pombe Puf1 in comple... -

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Basic information

Entry
Database: PDB / ID: 6ny5
TitleCrystal structure of the PUM-HD domain of S. pombe Puf1 in complex with RNA
Components
  • Pumilio domain-containing protein C56F2.08c
  • RNA (5'-R(P*UP*UP*AP*AP*UP*AP*AP*CP*UP*UP*AP*AP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / PUF protein / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


mRNA 3'-UTR AU-rich region binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / cytoplasmic stress granule / cytoplasm
Similarity search - Function
Npl3, RNA recognition motif 1 / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Npl3, RNA recognition motif 1 / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Pumilio domain-containing protein C56F2.08c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / Resolution: 3.002 Å
AuthorsQiu, C. / Hall, T.M.T.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.
Authors: Qiu, C. / Dutcher, R.C. / Porter, D.F. / Arava, Y. / Wickens, M. / Hall, T.M.T.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pumilio domain-containing protein C56F2.08c
B: Pumilio domain-containing protein C56F2.08c
C: RNA (5'-R(P*UP*UP*AP*AP*UP*AP*AP*CP*UP*UP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8469
Polymers93,3423
Non-polymers5056
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-83 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.677, 159.677, 215.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Pumilio domain-containing protein C56F2.08c / Puf1


Mass: 44634.555 Da / Num. of mol.: 2 / Fragment: PUM-HD domain (UNP residues 109-485)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPBC56F2.08c / Production host: Escherichia coli (E. coli) / References: UniProt: O60059
#2: RNA chain RNA (5'-R(P*UP*UP*AP*AP*UP*AP*AP*CP*UP*UP*AP*AP*U)-3')


Mass: 4072.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4 M magnesium sulfate, 0.1 M MES

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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 944+ / Detector: CCD / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28120 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.023 / Rrim(I) all: 0.066 / Χ2: 1.032 / Net I/σ(I): 12.4 / Num. measured all: 226676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.058.10.52613760.960.1970.5620.871100
3.05-3.118.20.44113750.9680.1650.4720.892100
3.11-3.178.20.39813790.9730.1490.4260.902100
3.17-3.238.20.31414050.9870.1170.3350.936100
3.23-3.38.20.31913740.9830.1190.340.94100
3.3-3.388.10.25513870.9890.0950.2730.956100
3.38-3.468.20.18613990.9930.0690.1980.996100
3.46-3.568.10.14813760.9960.0550.1581.06100
3.56-3.668.20.12514050.9960.0470.1341.09100
3.66-3.788.10.11513880.9970.0430.1231.212100
3.78-3.918.10.09313990.9970.0350.0991.048100
3.91-4.078.10.07813910.9980.0290.0841.199.9
4.07-4.268.10.06314030.9980.0240.0671.084100
4.26-4.4880.06114070.9990.0230.0651.177100
4.48-4.768.10.05314160.9980.020.0571.027100
4.76-5.138.10.04914120.9990.0190.0530.94999.9
5.13-5.6480.04914210.9990.0180.0521.0399.9
5.64-6.468.10.04314350.9990.0160.0460.991100
6.46-8.137.90.03214570.9990.0120.0341.20299.9
8.13-507.30.02315150.9990.0090.0251.16998.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementResolution: 3.002→32.759 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.61
RfactorNum. reflection% reflection
Rfree0.2634 1948 7.08 %
Rwork0.2109 --
obs0.2146 27506 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 214.33 Å2 / Biso mean: 93.1287 Å2 / Biso min: 36.81 Å2
Refinement stepCycle: final / Resolution: 3.002→32.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6099 272 26 25 6422
Biso mean--130.72 65.71 -
Num. residues----769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0016-3.07660.35341420.28731814195699
3.0766-3.15970.3111410.284718221963100
3.1597-3.25260.35741410.27351824196599
3.2526-3.35750.42691330.28931811194498
3.3575-3.47740.33981430.27331811195498
3.4774-3.61640.34821360.24611788192497
3.6164-3.78080.29311370.23951791192897
3.7808-3.97980.25091450.2231782192796
3.9798-4.22870.2241310.19521795192696
4.2287-4.55440.21241320.17861799193197
4.5544-5.01120.23111360.17861810194696
5.0112-5.7330.25581390.21011835197498
5.733-7.21030.26211480.21611891203999
7.2103-32.76050.21961440.17081985212999
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)
12.7695-1.26452.11690.8657-0.65572.8723-0.04050.0121-0.1065-0.0534-0.03560.20650.2096-0.33830.11310.4674-0.1022-0.00450.46440.01890.752656.366468.862255.1365
21.6503-0.74811.10832.45-0.03653.49510.21150.4968-0.1811-0.3451-0.22730.12320.07010.18580.04130.39940.04170.0080.7021-0.08080.4508111.751456.307337.2712
34.4458-1.00740.10930.54320.39271.32170.05531.54310.0208-0.58560.08740.0997-0.07220.7848-0.16420.7750.00980.09951.00490.01410.796184.581557.319551.0845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 97 through 482)A97 - 482
2X-RAY DIFFRACTION2(chain 'B' and resid 97 through 478)B97 - 478
3X-RAY DIFFRACTION3(chain 'C' and resid -1 through 12)C-1 - 12

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