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- PDB-6nx5: Crystal structure of the RRM domain of S. pombe Puf1 in the P21 s... -

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Basic information

Entry
Database: PDB / ID: 6nx5
TitleCrystal structure of the RRM domain of S. pombe Puf1 in the P21 space group
ComponentsPumilio domain-containing protein C56F2.08c
KeywordsRNA BINDING PROTEIN / the 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 ...: / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.554 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 8, 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 1.2Mar 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

Downloads & links

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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)35,5726
Polymers35,4484
Non-polymers1242
Water4,161231
1
A: Pumilio domain-containing protein C56F2.08c
B: Pumilio domain-containing protein C56F2.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8484
Polymers17,7242
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-14 kcal/mol
Surface area8070 Å2
MethodPISA
2
C: Pumilio domain-containing protein C56F2.08c
D: Pumilio domain-containing protein C56F2.08c


Theoretical massNumber of molelcules
Total (without water)17,7242
Polymers17,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-13 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.854, 37.592, 73.930
Angle α, β, γ (deg.)90.000, 94.200, 90.000
Int Tables number4
Space group name H-MP1211

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.83 Å3/Da / Density % sol: 32.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 15% w/v PEG3350, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 18, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 36421 / % possible obs: 98.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.029 / Rrim(I) all: 0.068 / Χ2: 0.904 / Net I/σ(I): 13.2 / Num. measured all: 201031
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.5850.54916550.8430.260.610.85890.9
1.58-1.615.20.46817890.8790.2220.520.87396.7
1.61-1.645.40.4417780.8820.2070.4880.85696.9
1.64-1.675.50.38318620.9170.1790.4240.88999.9
1.67-1.715.60.32317960.9390.150.3570.8997.7
1.71-1.755.60.25918090.9560.120.2870.958100
1.75-1.795.60.21518260.9680.10.2380.93698.2
1.79-1.845.60.18418320.9740.0850.2031100
1.84-1.895.60.15618220.9810.0720.1721.04798.8
1.89-1.955.60.12818510.9850.0590.1411.036100
1.95-2.025.70.1118200.9870.050.1211.04799.2
2.02-2.15.60.09618670.9880.0440.1061.03499.5
2.1-2.25.60.08318360.9910.0380.0920.96999.9
2.2-2.325.70.07518530.9920.0340.0820.89199.8
2.32-2.465.60.07118540.9920.0320.0780.87499.9
2.46-2.655.60.06818580.9920.0310.0750.86999.9
2.65-2.925.60.06318770.9920.0290.0690.82699.9
2.92-3.345.60.05818720.9940.0270.0640.72799.8
3.34-4.215.50.05418650.9930.0260.060.71798.6
4.21-5050.05616990.9910.0290.0630.73987.1

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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 / Resolution: 1.554→38.222 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2009 6.01 %
Rwork0.1927 31394 -
obs0.195 33403 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.84 Å2 / Biso mean: 24.5852 Å2 / Biso min: 2.04 Å2
Refinement stepCycle: final / Resolution: 1.554→38.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 8 231 2564
Biso mean--34.5 30.61 -
Num. residues----309
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 (%)
1.5537-1.59250.2279790.20281242132151
1.5925-1.63560.23621100.21161593170364
1.6356-1.68370.25891050.21061864196974
1.6837-1.73810.24851450.20962055220083
1.7381-1.80020.23971420.20842306244892
1.8002-1.87230.27021570.21592458261599
1.8723-1.95750.2371640.20532468263299
1.9575-2.06070.23211470.19722519266699
2.0607-2.18980.22191640.193624602624100
2.1898-2.35880.25361610.194125082669100
2.3588-2.59610.23371600.197725102670100
2.5961-2.97170.26741650.197125232688100
2.9717-3.74350.19391610.17425342695100
3.7435-38.23360.21841490.17972354250390
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)
10.8370.0939-0.05310.58880.01780.47220.0366-0.02160.102-0.1308-0.00120.49870.0096-0.2863-0.02130.0089-0.0319-0.09890.11450.0130.298-16.94516.4585-7.3454
20.95440.06330.67821.38760.1420.9154-0.07950.1470.054-0.4502-0.01710.1080.0277-0.01580.04060.1327-0.0067-0.01970.0506-0.00080.0341-5.093619.5454-13.0153
32.97180.0381-0.88412.39040.86892.909-0.12640.0075-0.2412-0.50290.0021-0.38890.3091-0.0250.07870.2194-0.01320.06120.0934-0.01090.1404-39.0704-3.5936-23.0704
42.1101-1.6108-1.06431.32630.43672.1442-0.080.22870.0967-0.64390.0988-0.9014-0.08060.3141-0.4310.3939-0.01570.27510.1987-0.03340.3852-25.50869.5032-29.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -3 through 79)A-3 - 79
2X-RAY DIFFRACTION2(chain 'B' and resid -1 through 75)B-1 - 75
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 75)C0 - 75
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 74)D0 - 74

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