6QZH

Structure of the human CC Chemokine Receptor 7 in complex with the intracellular allosteric antagonist Cmp2105 and the insertion protein Sialidase NanA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7.

Jaeger, K.Bruenle, S.Weinert, T.Guba, W.Muehle, J.Miyazaki, T.Weber, M.Furrer, A.Haenggi, N.Tetaz, T.Huang, C.Y.Mattle, D.Vonach, J.M.Gast, A.Kuglstatter, A.Rudolph, M.G.Nogly, P.Benz, J.Dawson, R.J.P.Standfuss, J.

(2019) Cell 178: 1222-1230.e10

  • DOI: 10.1016/j.cell.2019.07.028
  • Primary Citation of Related Structures:  
    6QZH

  • PubMed Abstract: 
  • The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we pr ...

    The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer.


    Organizational Affiliation

    Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI. Electronic address: joerg.standfuss@psi.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7A785Homo sapiensStreptococcus pneumoniaeMutation(s): 1 
Gene Names: CCR7CMKBR7EBI1EVI1
EC: 3.2.1.18
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
CCR7 chemokine receptor in complex with Cmp2105
Find proteins for P62576 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P62576 
Go to UniProtKB:  P62576
Find proteins for P32248 (Homo sapiens)
Explore P32248 
Go to UniProtKB:  P32248
NIH Common Fund Data Resources
PHAROS  P32248
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JLW
Query on JLW

Download CCD File 
A
3-[[4-[[(1~{R})-2,2-dimethyl-1-(5-methylfuran-2-yl)propyl]amino]-1,1-bis(oxidanylidene)-1,2,5-thiadiazol-3-yl]amino]-~{N},~{N},6-trimethyl-2-oxidanyl-benzamide
C22 H29 N5 O5 S
MAYXLCLBDVEYAL-SFHVURJKSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TAR
Query on TAR

Download CCD File 
A
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JLWKd:  3   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.124α = 90
b = 128.809β = 90
c = 100.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission701647
Swiss National Science FoundationSwitzerland31003A_159558

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references, Source and taxonomy, Structure summary