Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 89.29 kDa 
• Atom Count: 6116 
• Modelled Residue Count: 744 
• Deposited Residue Count: 785 
• Unique protein chains: 1

6QZH

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

• PDB DOI: 10.2210/pdb6QZH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Streptococcus pneumoniae
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2019-03-11 Released: 2019-09-04 
• Deposition Author(s): 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.
• Funding Organization(s): European Commission, Swiss National Science Foundation

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Experimental Data Snapshot

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

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

• PubMed: 31442409 
• 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 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.

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Organizational Affiliation: 

Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7	A	785	Homo sapiens, Streptococcus pneumoniae	Mutation(s): 1  Gene Names: CCR7, CMKBR7, EBI1, EVI1, nanA EC: 3.2.1.18 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
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
PHAROS:  P32248
UniProt Groups	P32248P62576

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JLW	C [auth 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
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TAR	E [auth A], F [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JLW	Binding MOAD:  6QZH	Kd: 3 (nM) from 1 assay(s)

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 = 79.124	α = 90
b = 128.809	β = 90
c = 100.576	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-11 
• Released Date: 2019-09-04 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
European Commission		701647
Swiss National Science Foundation	Switzerland	31003A_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