RCSB PDB - 9D3E: Cryo-EM structure of CCR6 bound by SQA1 and OXM2

 9D3E

Cryo-EM structure of CCR6 bound by SQA1 and OXM2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for CCR6 modulation by allosteric antagonists.

Wasilko, D.J.Gerstenberger, B.S.Farley, K.A.Li, W.Alley, J.Schnute, M.E.Unwalla, R.J.Victorino, J.Crouse, K.K.Ding, R.Sahasrabudhe, P.V.Vincent, F.Frisbie, R.K.Dermenci, A.Flick, A.Choi, C.Chinigo, G.Mousseau, J.J.Trujillo, J.I.Nuhant, P.Mondal, P.Lombardo, V.Lamb, D.Hogan, B.J.Minhas, G.S.Segala, E.Oswald, C.Windsor, I.W.Han, S.Rappas, M.Cooke, R.M.Calabrese, M.F.Berstein, G.Thorarensen, A.Wu, H.

(2024) Nat Commun 15: 7574-7574

  • DOI: https://doi.org/10.1038/s41467-024-52045-7
  • Primary Citation of Related Structures:  
    9D3E, 9D3G

  • PubMed Abstract: 

    The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.


  • Organizational Affiliation

    Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human CCR6480Homo sapiensMutation(s): 0 
Gene Names: CCR6
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Heavy chainB [auth H]269Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab NanobodyC [auth K]141synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Light chainD [auth L]233Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EBX (Subject of Investigation/LOI)
Query on EBX

Download Ideal Coordinates CCD File 
F [auth A]4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide
C22 H26 N4 O5
JSZQMZJVSCVDMA-CYBMUJFWSA-N
A1A1W (Subject of Investigation/LOI)
Query on A1A1W

Download Ideal Coordinates CCD File 
G [auth A]N-{[(2R)-4-(bicyclo[1.1.1]pentan-1-yl)-5-oxomorpholin-2-yl]methyl}-1-[4-(trifluoromethyl)phenyl]cyclopropane-1-carboxamide
C21 H23 F3 N2 O3
MGXLQVNOTOHKMK-VVFCZOMOSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
E [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary