7TE8 | pdb_00007te8

CA14-CBD-DB21 ternary complex

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-01-04 Released: 2022-01-12 
  • Deposition Author(s): Cao, S., Zheng, N.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.180 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Defining molecular glues with a dual-nanobody cannabidiol sensor.

Cao, S.Kang, S.Mao, H.Yao, J.Gu, L.Zheng, N.

(2022) Nat Commun 13: 815-815

  • DOI: https://doi.org/10.1038/s41467-022-28507-1
  • Primary Citation Related Structures: 
    7TE8

  • PubMed Abstract: 

    "Molecular glue" (MG) is a term coined to describe the mechanism of action of the plant hormone auxin and subsequently used to characterize synthetic small molecule protein degraders exemplified by immune-modulatory imide drugs (IMiDs). Prospective development of MGs, however, has been hampered by its elusive definition and thermodynamic characteristics. Here, we report the crystal structure of a dual-nanobody cannabidiol-sensing system, in which the ligand promotes protein-protein interaction in a manner analogous to auxin. Through quantitative analyses, we draw close parallels among the dual-nanobody cannabidiol sensor, the auxin perception complex, and the IMiDs-bound CRL4 CRBN E3, which can bind and ubiquitinate "neo-substrates". All three systems, including the recruitment of IKZF1 and CK1α to CRBN, are characterized by the lack of ligand binding activity in at least one protein partner and an under-appreciated preexisting low micromolar affinity between the two proteinaceous subunits that is enhanced by the ligand to reach the nanomolar range. These two unifying features define MGs as a special class of proximity inducers distinct from bifunctional compounds and can be used as criteria to guide target selection for future rational discovery of MGs.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 53.55 kDa 
  • Atom Count: 4,082 
  • Modeled Residue Count: 478 
  • Deposited Residue Count: 480 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CA14A [auth C],
C [auth D]
120synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DB21B [auth A],
D [auth B]
120synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.180 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.672α = 90
b = 69.153β = 90
c = 109.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM128918
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR21DA051555
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR21DA051194

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Source and taxonomy
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary