5LOP | pdb_00005lop

Structure of the active form of /K. lactis/ Dcp1-Dcp2-Edc3 decapping complex bound to m7GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.266 (Depositor), 0.314 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

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Literature

Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m(7)GDP and its Edc3 activator.

Charenton, C.Taverniti, V.Gaudon-Plesse, C.Back, R.Seraphin, B.Graille, M.

(2016) Nat Struct Mol Biol 23: 982-986

  • DOI: https://doi.org/10.1038/nsmb.3300
  • Primary Citation Related Structures: 
    5LON, 5LOP

  • PubMed Abstract: 

    Elimination of the 5' cap of eukaryotic mRNAs, known as decapping, is considered to be a crucial, irreversible and highly regulated step required for the rapid degradation of mRNA by Xrn1, the major cytoplasmic 5'-3' exonuclease. Decapping is accomplished by the recruitment of a protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor. However, this complex has a low intrinsic enzymatic activity and requires several accessory proteins such as the Lsm1-7 complex, Pat1, Edc1-Edc2 and/or Edc3 to be fully active. Here we present the crystal structure of the active form of the yeast Kluyveromyces lactis Dcp1-Dcp2 enzyme bound to its product (m 7 GDP) and its potent activator Edc3. This structure of the Dcp1-Dcp2 complex bound to a cap analog further explains previously published data on substrate binding and provides hints as to the mechanism of Edc3-mediated Dcp2 activation.


  • Organizational Affiliation
    • Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France.

Macromolecule Content 

  • Total Structure Weight: 62.43 kDa 
  • Atom Count: 4,075 
  • Modeled Residue Count: 494 
  • Deposited Residue Count: 535 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0F23980p281Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F23980g
UniProt
Find proteins for Q6CIU1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CIU1 
Go to UniProtKB:  Q6CIU1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CIU1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0E01827p188Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E01827g
UniProt
Find proteins for Q6CPV9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CPV9 
Go to UniProtKB:  Q6CPV9
Entity Groups
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UniProt GroupQ6CPV9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
KLLA0A11308p66Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_A11308g
UniProt
Find proteins for Q6CX48 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CX48 
Go to UniProtKB:  Q6CX48
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CX48
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.266 (Depositor), 0.314 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.81α = 90
b = 219.81β = 90
c = 74.19γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-11-BSV800902

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary