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- PDB-6ez7: Pes4 RRM3 Structure -

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Basic information

Entry
Database: PDB / ID: 6ez7
TitlePes4 RRM3 Structure
ComponentsProtein PES4
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif (RRM)
Function / homology
Function and homology information


mRNA localization resulting in post-transcriptional regulation of gene expression / Deadenylation of mRNA / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...mRNA localization resulting in post-transcriptional regulation of gene expression / Deadenylation of mRNA / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / Translation initiation complex formation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex / nucleus / cytosol
Similarity search - Function
RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein PES4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMohamad, N. / Bravo, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF 2015-67077-R Spain
CitationJournal: To Be Published
Title: Pes4 RRM3 Structure
Authors: Mohamad, N. / Bravo, J.
History
DepositionNov 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Protein PES4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9753
Polymers9,7631
Non-polymers2122
Water82946
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint5 kcal/mol
Surface area5530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.826, 82.826, 31.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

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Components

#1: Protein Protein PES4 / DNA polymerase epsilon suppressor 4


Mass: 9763.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PES4, YFR023W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39684
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsprotein used to set for the crystallization plates was Pes4(303-473) however, the part that ...protein used to set for the crystallization plates was Pes4(303-473) however, the part that crystallized was Pes4(303-384)

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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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 mM Ammonium Sulfate, 30% PEG 8000, 1M MES/NaOH pH 7.4 (additive)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.9→29.212 Å / Num. obs: 10165 / % possible obs: 99.99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.2455 / Rrim(I) all: 0.2546 / Net I/σ(I): 6.63
Reflection shellResolution: 1.9→1.94 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D77

5d77


Resolution: 1.9→29.212 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.2244 486 4.91 %
Rwork0.1945 --
obs0.1962 9907 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms665 0 14 46 725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003702
X-RAY DIFFRACTIONf_angle_d0.717940
X-RAY DIFFRACTIONf_dihedral_angle_d13.867266
X-RAY DIFFRACTIONf_chiral_restr0.032103
X-RAY DIFFRACTIONf_plane_restr0.003117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-2.17520.28551300.20953013X-RAY DIFFRACTION94
2.1752-2.74030.22461670.22273132X-RAY DIFFRACTION99
2.7403-29.21580.21521890.183276X-RAY DIFFRACTION100
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)
10.56960.0202-0.05050.54410.27910.9228-0.06580.03590.00160.10360.0296-0.1537-0.226-0.18740.00220.11440.0764-0.01340.2126-0.00780.127728.881531.004714.0585
20.1483-0.1921-0.18180.13920.05610.1289-0.00650.2102-0.1796-0.1954-0.0359-0.11740.0779-0.1750.00090.20660.05980.00870.2313-0.03380.167930.904426.72434.9287
30.21250.11420.07680.2141-0.02830.0478-0.26510.35360.0455-0.26310.05470.0121-0.6405-0.4158-0.01810.26130.2426-0.10310.5147-0.00550.136714.075335.3394.6914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 302 through 351 )
2X-RAY DIFFRACTION2chain 'A' and (resid 352 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 384 )

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