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- PDB-5jp4: Crystal structure of S. pombe Dcp1 in complex with the decapping ... -

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Basic information

Entry
Database: PDB / ID: 5jp4
TitleCrystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC
Components
  • Uncharacterized protein C18G6.09c
  • mRNA-decapping enzyme subunit 1
KeywordsPEPTIDE BINDING PROTEIN / EVH1 / complex / mRNA / decapping / Hydrolase
Function / homology
Function and homology information


mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process / P-body / mRNA processing / cytoplasmic stress granule / RNA binding ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process / P-body / mRNA processing / cytoplasmic stress granule / RNA binding / nucleus / cytosol
Similarity search - Function
: / Proline-rich nuclear receptor coactivator motif / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein C18G6.09c / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å
AuthorsWurm, J.P. / Sprangers, R.
CitationJournal: Rna / Year: 2016
Title: The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface.
Authors: Wurm, J.P. / Overbeck, J. / Sprangers, R.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary
Revision 1.2Mar 22, 2023Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping enzyme subunit 1
B: Uncharacterized protein C18G6.09c


Theoretical massNumber of molelcules
Total (without water)19,3432
Polymers19,3432
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-13 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.179, 41.452, 95.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15130.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcp1, SPBC3B9.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P805
#2: Protein/peptide Uncharacterized protein C18G6.09c


Mass: 4212.566 Da / Num. of mol.: 1 / Fragment: UNP Residues 156-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC18G6.09c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10108
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M NaCl, 100 mM NaCitrate pH 5-6 / PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→47.813 Å / Num. obs: 10434 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QKL

2qkl


Resolution: 2.043→47.813 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2221 523 5.03 %
Rwork0.1957 --
obs0.197 10391 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.043→47.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 0 43 1214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071212
X-RAY DIFFRACTIONf_angle_d0.8621651
X-RAY DIFFRACTIONf_dihedral_angle_d16.838722
X-RAY DIFFRACTIONf_chiral_restr0.058187
X-RAY DIFFRACTIONf_plane_restr0.005212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0426-2.24820.29321280.24292395X-RAY DIFFRACTION100
2.2482-2.57350.22791300.20782434X-RAY DIFFRACTION100
2.5735-3.24220.2381270.20052452X-RAY DIFFRACTION100
3.2422-47.82610.20171380.18132587X-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)
13.2776-0.19042.09635.8853.36536.3963-0.24670.3303-0.0296-0.80290.0936-0.04360.2767-0.06590.17120.512-0.08610.02830.38210.08560.17716.716118.2678101.2603
25.5974-0.4161-2.1044.5655-0.08416.63080.0772-0.03650.3055-0.1163-0.02110.4563-0.5093-0.307-0.06550.1817-0.02170.00010.15630.01360.26929.692318.0151118.8336
33.35260.17720.32274.8784-1.16675.31630.07190.06450.1157-0.2527-0.0075-0.0753-0.0501-0.1205-0.02330.2342-0.00720.01690.1295-0.00450.208517.505318.9525116.4687
44.6435-2.033-0.79325.33920.10453.7130.0691-0.2673-0.28170.2126-0.02490.1252-0.0229-0.0539-0.05160.2381-0.0320.01030.19220.01840.204614.755210.6086120.583
55.11450.46195.7054.8198-1.37617.11140.1817-0.16440.58351.0673-0.39810.03320.00320.361-0.12890.370.0612-0.02480.7735-0.20990.53968.098112.774128.7445
63.09070.2081-0.19938.36930.41460.7593-0.3664-0.7564-0.3181.45680.2731-0.50410.2307-0.3394-0.00420.8570.09990.31380.48170.01930.33139.124314.7807133.8628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 127 )
5X-RAY DIFFRACTION5chain 'B' and (resid 142 through 168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 179 )

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