4BY6

Yeast Not1-Not2-Not5 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and RNA-Binding Properties of the not1-not2-not5 Module of the Yeast Ccr4-not Complex

Bhaskar, V.Roudko, V.Basquin, J.Sharma, K.Urlaub, H.Seraphin, B.Conti, E.

(2013) Nat Struct Mol Biol 20: 1281

  • DOI: https://doi.org/10.1038/nsmb.2686
  • Primary Citation of Related Structures:  
    4BY6

  • PubMed Abstract: 

    The Ccr4-Not complex is involved in several aspects of gene expression, including mRNA decay, translational repression and transcription. We determined the 2.8-Å-resolution crystal structure of a 120-kDa core complex of the Saccharomyces cerevisiae Not module comprising the C-terminal arm of Not1, Not2 and Not5. Not1 is a HEAT-repeat scaffold. Not2 and Not5 have extended regions that wrap around Not1 and around their globular domains, the Not boxes. The Not boxes resemble Sm folds and interact with each other with a noncanonical dimerization surface. Disruption of the interactions within the ternary complex has severe effects on growth in vivo. The ternary complex forms a composite surface that binds poly(U) RNA in vitro, with a site at the Not5 Not box. The results suggest that the Not module forms a versatile platform for macromolecular interactions.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry (MPI Biochemistry), Martinsried, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
A, D
553Saccharomyces cerevisiae CEN.PK113-7DMutation(s): 0 
UniProt
Find proteins for P25655 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25655 
Go to UniProtKB:  P25655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25655
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2
B, E
191Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P06100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06100 
Go to UniProtKB:  P06100
Entity Groups  
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UniProt GroupP06100
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5
C, F
262Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12514 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12514 
Go to UniProtKB:  Q12514
Entity Groups  
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UniProt GroupQ12514
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth C],
N [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B],
M [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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H [auth A],
L [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.452α = 90
b = 109.174β = 94.7
c = 133.622γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other