5AMH

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Dynamics of the Cereblon Ligand Binding Domain.

Hartmann, M.D.Boichenko, I.Coles, M.Lupas, A.N.Hernandez Alvarez, B.

(2015) Plos One 10: 28342

  • DOI: 10.1371/journal.pone.0128342
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different o ...

    Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution.


    Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CEREBLON ISOFORM 4
A
125Magnetospirillum gryphiswaldenseMutation(s): 0 
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Go to UniProtKB:  A4TVL0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EF2
Query on EF2

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A
S-Thalidomide
C13 H10 N2 O4
UEJJHQNACJXSKW-VIFPVBQESA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EF2Ki: 4400 nM (100) BINDINGDB
EF2IC50: 7800 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.720α = 90.00
b = 51.720β = 90.00
c = 84.710γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release