5AMK | pdb_00005amk

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form

PDB DOI: https://doi.org/10.2210/pdb5AMK/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.217 (Depositor), 0.198 (DCC)
R-Value Work:
0.175 (Depositor)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 26024445 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 55.67 kDa
Atom Count: 3,411
Modeled Residue Count: 422
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CEREBLON ISOFORM 4	A, B, C, D	125	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense) Explore A4TVL0 Go to UniProtKB: A4TVL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4TVL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EF2 Query on EF2 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	S-Thalidomide C₁₃ H₁₀ N₂ O₄ UEJJHQNACJXSKW-VIFPVBQESA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
DMS	BindingDB: 5AMK	Ki: min: 1.07e+4, max: 1.10e+7 (nM) from 3 assay(s)
DMS	BindingDB: 5AMK	IC50: 2.08e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.217 (Depositor), 0.198 (DCC)
R-Value Work: 0.175 (Depositor)
R-Value Observed: 0.177 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.86	α = 90
b = 137.86	β = 90
c = 154.39	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Hartmann, M.D.

Lupas, A.N.

Hernandez Alvarez, B.

Revision History (Full details and data files)

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