4GMJ

Structure of human NOT1 MIF4G domain co-crystallized with CAF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex

Petit, A.P.Wohlbold, L.Bawankar, P.Huntzinger, E.Schmidt, S.Izaurralde, E.Weichenrieder, O.

(2012) Nucleic Acids Res 40: 11058-11072

  • DOI: https://doi.org/10.1093/nar/gks883
  • Primary Citation of Related Structures:  
    4GMJ, 4GML

  • PubMed Abstract: 

    The CCR4-NOT complex plays a crucial role in post-transcriptional mRNA regulation in eukaryotic cells. It catalyzes the removal of mRNA poly(A) tails, thereby repressing translation and committing mRNAs to decay. The conserved core of the complex consists of a catalytic module comprising two deadenylases (CAF1/POP2 and CCR4a/b) and the NOT module, which contains at least NOT1, NOT2 and NOT3. NOT1 bridges the interaction between the two modules and therefore, acts as a scaffold protein for the assembly of the complex. Here, we present the crystal structures of the CAF1-binding domain of human NOT1 alone and in complex with CAF1. The NOT1 domain comprises five helical hairpins that adopt an MIF4G (middle portion of eIF4G) fold. This NOT1 MIF4G domain binds CAF1 through a pre-formed interface and leaves the CAF1 catalytic site fully accessible to RNA substrates. The conservation of critical structural and interface residues suggests that the NOT1 MIF4G domain adopts a similar fold and interacts with CAF1 in a similar manner in all eukaryotes. Our findings shed light on the assembly of the CCR4-NOT complex and provide the basis for dissecting the role of the NOT module in mRNA deadenylation.


  • Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 1
A, C, E
229Homo sapiensMutation(s): 0 
Gene Names: AD-005CDC39CNOT1KIAA1007NOT1
UniProt & NIH Common Fund Data Resources
Find proteins for A5YKK6 (Homo sapiens)
Explore A5YKK6 
Go to UniProtKB:  A5YKK6
PHAROS:  A5YKK6
GTEx:  ENSG00000125107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5YKK6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 7
B, D, F
285Homo sapiensMutation(s): 0 
Gene Names: CAF1CNOT7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIV1 (Homo sapiens)
Explore Q9UIV1 
Go to UniProtKB:  Q9UIV1
PHAROS:  Q9UIV1
GTEx:  ENSG00000198791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B],
N [auth D],
R [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth B],
O [auth D],
S [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
K [auth B]
L [auth D]
M [auth D]
G [auth B],
H [auth B],
K [auth B],
L [auth D],
M [auth D],
P [auth F],
Q [auth F],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.47α = 90
b = 101.74β = 101.1
c = 142.2γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description