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- PDB-5j3t: Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex -

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Basic information

Entry
Database: PDB / ID: 5j3t
TitleCrystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex
Components
  • Edc1
  • mRNA decapping complex subunit 2
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / decapping / mRNA decay / EVH1 / Nudix
Function / homology
Function and homology information


mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process / meiotic cell cycle / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proline-rich nuclear receptor coactivator motif / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. ...Proline-rich nuclear receptor coactivator motif / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / mRNA decapping complex subunit 2 / Uncharacterized protein C18G6.09c / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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: mRNA decapping complex subunit 2
C: Edc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6919
Polymers46,4363
Non-polymers2546
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-29 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.809, 41.371, 93.718
Angle α, β, γ (deg.)90.00, 114.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21B-421-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15294.453 Da / Num. of mol.: 1
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 mRNA decapping complex subunit 2


Mass: 28399.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: dcp2, SPAC19A8.12 / Plasmid: pnYC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: O13828, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Edc1


Mass: 2742.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10108

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Non-polymers , 3 types, 221 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.8
Details: 1.55 M sodium formate, 0.1 M sodium acetate (pH 4.8)

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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 19, 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: 1.6→45.1 Å / Num. obs: 45926 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.59 Å2 / Rsym value: 0.028 / Net I/σ(I): 18.9
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.653 / % possible all: 96.4

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Processing

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

5j3y


Resolution: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.9505 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.099 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 2288 5 %RANDOM
Rwork0.186 ---
obs0.1876 45762 99.42 %-
Displacement parametersBiso mean: 40.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.8139 Å20 Å21.6285 Å2
2---0.0984 Å20 Å2
3---0.9123 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 16 215 3470
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054539HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1177SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes486HARMONIC5
X-RAY DIFFRACTIONt_it3343HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion16.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion427SEMIHARMONIC5
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_contact4151SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2669 167 5 %
Rwork0.2475 3173 -
all0.2485 3340 -
obs--98.46 %
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)
12.2324-1.011-0.71642.32130.2350.9371-0.0563-0.1835-0.0511-0.14540.088-0.31180.04290.0761-0.0317-0.086-0.00070.0247-0.0831-0.0112-0.010620.102322.08344.2633
20.4840.25970.94070.53290.51751.6901-0.1093-0.06660.05810.10310.02820.0622-0.1746-0.05110.0811-0.02310.0112-0.0063-0.0207-0.0016-0.087410.901938.679227.6891
30.66810.3587-0.67313.70510.24090.95790.0219-0.0587-0.10890.0779-0.0528-0.57560.04890.58820.0309-0.13760.0479-0.10540.13590.0173-0.098725.355823.195217.7057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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