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Basic information

Entry
Database: PDB / ID: 5n2v
TitleChanges in conformational equilibria regulate the activity of the Dcp2 decapping enzyme
Components
  • Edc1
  • mRNA decapping complex subunit 2
  • mRNA-decapping enzyme subunit 1
KeywordsRNA BINDING PROTEIN
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 / : ...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 / 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) / NUDIX domain / PH-domain like / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / 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: 3.1 Å
AuthorsHoldermann, I. / Sprangers, R.
Funding support1items
OrganizationGrant numberCountry
EUERC-616052
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme.
Authors: Wurm, J.P. / Holdermann, I. / Overbeck, J.H. / Mayer, P.H.O. / Sprangers, R.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.0Feb 28, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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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
D: mRNA-decapping enzyme subunit 1
E: mRNA decapping complex subunit 2
F: Edc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,18714
Polymers93,1236
Non-polymers1,0648
Water0
1
A: mRNA-decapping enzyme subunit 1
B: mRNA decapping complex subunit 2
C: Edc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0947
Polymers46,5623
Non-polymers5324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-65 kcal/mol
Surface area17960 Å2
MethodPISA
2
D: mRNA-decapping enzyme subunit 1
E: mRNA decapping complex subunit 2
F: Edc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0947
Polymers46,5623
Non-polymers5324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-64 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.841, 76.522, 89.526
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15130.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcp1, SPBC3B9.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P805
#2: Protein mRNA decapping complex subunit 2


Mass: 28689.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcp2, SPAC19A8.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O13828, Hydrolases
#3: Protein/peptide Edc1


Mass: 2742.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10108
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O11P2

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 41% M1K3350 Morpheus Mix 4, MOPS pH 7.0, 0.06 M MgCl2/CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.1→48.3 Å / Num. obs: 15440 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.95 / Rmerge(I) obs: 0.24 / Net I/σ(I): 4.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j3t

5j3t


Resolution: 3.1→48.289 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97
RfactorNum. reflection% reflection
Rfree0.2868 802 5.2 %
Rwork0.2388 --
obs0.2414 15409 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 64 0 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026336
X-RAY DIFFRACTIONf_angle_d0.4878594
X-RAY DIFFRACTIONf_dihedral_angle_d14.8693784
X-RAY DIFFRACTIONf_chiral_restr0.043930
X-RAY DIFFRACTIONf_plane_restr0.0031118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29420.33611260.26282409X-RAY DIFFRACTION100
3.2942-3.54850.34071430.26492426X-RAY DIFFRACTION100
3.5485-3.90540.31241190.2362426X-RAY DIFFRACTION100
3.9054-4.47020.26171470.22152415X-RAY DIFFRACTION100
4.4702-5.63060.24511210.21972441X-RAY DIFFRACTION100
5.6306-48.29470.27231460.2482490X-RAY DIFFRACTION100

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