5AMH | pdb_00005amh

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

• PDB DOI: https://doi.org/10.2210/pdb5AMH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Magnetospirillum gryphiswaldense MSR-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-10 Released: 2015-07-01 
• Deposition Author(s): Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.157 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

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

• PubMed: 26024445 
• DOI: https://doi.org/10.1371/journal.pone.0128342
• Primary Citation Related Structures: 
  5AMH, 5AMI, 5AMJ, 5AMK


• 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 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.

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Organizational Affiliation: 
• Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.37 kDa 
• Atom Count: 1,060 
• Modeled Residue Count: 106 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CEREBLON ISOFORM 4	A	125	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense) Explore A4TVL0  Go to UniProtKB:  A4TVL0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EF2	C [auth A]	S-Thalidomide C13 H10 N2 O4 UEJJHQNACJXSKW-VIFPVBQESA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	L [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.157 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.72	α = 90
b = 51.72	β = 90
c = 84.71	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description