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- PDB-5j3q: Crystal structure of S. pombe Dcp1:Edc1 mRNA decapping complex -

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Basic information

Entry
Database: PDB / ID: 5j3q
TitleCrystal structure of S. pombe Dcp1:Edc1 mRNA decapping complex
Components
  • Edc1
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / decapping / mRNA decay / EVH1
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: 1.87 Å
AuthorsValkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.
Authors: Valkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping enzyme subunit 1
B: Edc1
C: mRNA-decapping enzyme subunit 1
D: Edc1


Theoretical massNumber of molelcules
Total (without water)36,0734
Polymers36,0734
Non-polymers00
Water2,558142
1
A: mRNA-decapping enzyme subunit 1
B: Edc1


Theoretical massNumber of molelcules
Total (without water)18,0372
Polymers18,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area7850 Å2
MethodPISA
2
C: mRNA-decapping enzyme subunit 1
D: Edc1


Theoretical massNumber of molelcules
Total (without water)18,0372
Polymers18,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.635, 70.085, 96.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15294.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcp1, SPBC3B9.21 / Plasmid: pnEApG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q9P805
#2: Protein/peptide Edc1


Mass: 2742.089 Da / Num. of mol.: 2 / Fragment: UNP residues 155-180 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10108
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M PCB buffer (sodium propionate, sodium cacodylate and BIS-TRIS propane in a molar ratio of 2:1:2, (pH 6.0)), 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→19.54 Å / Num. obs: 24087 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3Y, CHAIN A

5j3y


Resolution: 1.87→19.54 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 1178 4.9 %RANDOM
Rwork0.2065 ---
obs0.2082 24032 99.8 %-
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7854 Å20 Å20 Å2
2---4.2228 Å20 Å2
3---0.4374 Å2
Refine analyzeLuzzati coordinate error obs: 0.279 Å
Refinement stepCycle: LAST / Resolution: 1.87→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 0 142 2452
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012372HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d813SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it2372HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion307SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2733SEMIHARMONIC4
LS refinement shellResolution: 1.87→1.95 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2493 151 5.24 %
Rwork0.2175 2733 -
all0.2191 2884 -
obs--99.83 %
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)
13.349-0.08590.19941.7280.08661.5897-0.0044-0.17870.20250.0313-0.0544-0.039-0.1366-0.04240.0588-0.1353-0.00020.00260.0011-0.0403-0.0922-16.7154-30.203914.7573
23.96632.2093-2.23571.7693-2.29111.08460.00670.25570.225-0.1561-0.0411-0.14740.03920.15170.0344-0.05120.1082-0.0186-0.0170.22060.035-13.8659-19.86882.0339
34.02480.6968-0.1331.64510.31631.7041-0.01260.0350.04780.0248-0.0201-0.0526-0.08570.04570.0326-0.12670.00270.008-0.0275-0.0173-0.0988-16.76854.9033-6.468
46.98870.5273-2.99572.7596-2.67462.65230.00990.28380.093-0.1602-0.0858-0.1435-0.03310.20760.0759-0.0337-0.04610.02450.00580.1298-0.0255-13.100118.1237-16.1719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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