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- PDB-6nww: Crystal structure of the RRM domain of S. pombe Puf1 in the P2121... -

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Basic information

Entry
Database: PDB / ID: 6nww
TitleCrystal structure of the RRM domain of S. pombe Puf1 in the P212121 space group
ComponentsPumilio domain-containing protein C56F2.08c
KeywordsRNA BINDING PROTEIN / RRM domain
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
Pumilio domain-containing protein C56F2.08c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 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 7, 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
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Pumilio domain-containing protein C56F2.08c
B: Pumilio domain-containing protein C56F2.08c
C: Pumilio domain-containing protein C56F2.08c
D: Pumilio domain-containing protein C56F2.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5196
Polymers35,4484
Non-polymers712
Water4,053225
1
A: Pumilio domain-containing protein C56F2.08c
B: Pumilio domain-containing protein C56F2.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7593
Polymers17,7242
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-26 kcal/mol
Surface area7610 Å2
MethodPISA
2
C: Pumilio domain-containing protein C56F2.08c
D: Pumilio domain-containing protein C56F2.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7593
Polymers17,7242
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-25 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.692, 63.896, 79.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8861.899 Da / Num. of mol.: 4 / Fragment: RRM domain (UNP residues 1-79)
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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.1 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.3 M sodium chloride, 0.1 M citric acid, 20% glycerol

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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: Jan 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 17513 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Χ2: 1.044 / Net I/σ(I): 9.2 / Num. measured all: 63326
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.06-2.12.20.2068380.965195.1
2.1-2.132.80.2038461.069199.2
2.13-2.173.20.2068821.034199.9
2.17-2.223.60.1798871.032199.9
2.22-2.273.70.1648741.0491100
2.27-2.323.70.1788771.111100
2.32-2.383.70.1488841.099199.9
2.38-2.443.70.1268621.0591100
2.44-2.513.70.1248901.174199.8
2.51-2.63.80.1258831.152199.7
2.6-2.693.80.1148791.017199.2
2.69-2.83.70.1088751.076199.2
2.8-2.923.80.0848811.011198.9
2.92-3.083.80.0778871.095198.7
3.08-3.273.80.0718771.056198
3.27-3.523.80.0628820.917197.6
3.52-3.883.90.0558690.954196.2
3.88-4.443.80.068800.998195.4
4.44-5.593.90.0538721.045194.1
5.59-503.80.0548880.948188.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NX5

6nx5


Resolution: 2.06→24.49 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.2251 1686 9.98 %
Rwork0.1722 --
obs0.1776 16888 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.44 Å2 / Biso mean: 20.9228 Å2 / Biso min: 1.13 Å2
Refinement stepCycle: final / Resolution: 2.06→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 2 225 2527
Biso mean--18.35 25.5 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0584-2.11890.27641280.19261171129989
2.1189-2.18730.23581330.17931256138994
2.1873-2.26540.2321400.16441251139195
2.2654-2.3560.26291430.17321256139995
2.356-2.46320.22831420.16811253139596
2.4632-2.59290.25221380.18161263140196
2.5929-2.75520.24791410.18391277141895
2.7552-2.96750.23211400.18691273141397
2.9675-3.26560.24821460.18411293143997
3.2656-3.73670.2121450.15741307145297
3.7367-4.70230.17581440.14871296144095
4.7023-24.49160.21081460.18111306145291
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)
13.0359-0.0124-0.15794.1052-0.76312.7466-0.04390.04140.00480.05310.02830.0603-0.15880.0487-0.00220.13230.01310.00240.09-0.03010.0731-29.022.990830.9009
22.85460.0740.44132.4674-0.36781.9257-0.01810.0252-0.1184-0.0177-0.0112-0.04790.09590.07460.0190.0911-0.00220.0180.0855-0.01550.0478-27.02268.715811.4326
33.2961-0.4225-0.34093.0262-0.29731.9924-0.06280.14480.05830.0371-0.0317-0.0282-0.10230.10790.09340.0914-0.0153-0.01280.0690.0070.0588-2.5178-14.917330.7812
44.0273-1.3199-0.73064.9794-1.23013.6148-0.01310.2418-0.1097-0.1837-0.149-0.00240.222-0.12330.13960.1569-0.02090.02380.17940.02190.1065-1.4126-9.018311.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 75)A0 - 75
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 75)B0 - 75
3X-RAY DIFFRACTION3(chain 'C' and resid -2 through 75)C-2 - 75
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 75)D0 - 75

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