8TLM | pdb_00008tlm

Structure of a class A GPCR/Fab complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TLM

This is version 1.1 of the entry. See complete history

Literature

Structural basis of antibody inhibition and chemokine activation of the human CC chemokine receptor 8.

Sun, D.Sun, Y.Janezic, E.Zhou, T.Johnson, M.Azumaya, C.Noreng, S.Chiu, C.Seki, A.Arenzana, T.L.Nicoludis, J.M.Shi, Y.Wang, B.Ho, H.Joshi, P.Tam, C.Payandeh, J.Comps-Agrar, L.Wang, J.Rutz, S.Koerber, J.T.Masureel, M.

(2023) Nat Commun 14: 7940-7940

  • DOI: https://doi.org/10.1038/s41467-023-43601-8
  • Primary Citation Related Structures: 
    8TLM, 8U1U

  • PubMed Abstract: 

    The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein coupled receptor that has emerged as a promising therapeutic target in cancer. Targeting CCR8 with an antibody has appeared to be an attractive therapeutic approach, but the molecular basis for chemokine-mediated activation and antibody-mediated inhibition of CCR8 are not fully elucidated. Here, we obtain an antagonist antibody against human CCR8 and determine structures of CCR8 in complex with either the antibody or the endogenous agonist ligand CCL1. Our studies reveal characteristic antibody features allowing recognition of the CCR8 extracellular loops and CCL1-CCR8 interaction modes that are distinct from other chemokine receptor - ligand pairs. Informed by these structural insights, we demonstrate that CCL1 follows a two-step, two-site binding sequence to CCR8 and that antibody-mediated inhibition of CCL1 signaling can occur by preventing the second binding event. Together, our results provide a detailed structural and mechanistic framework of CCR8 activation and inhibition that expands our molecular understanding of chemokine - receptor interactions and offers insight into the development of therapeutic antibodies targeting chemokine GPCRs.


  • Organizational Affiliation
    • Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 123.18 kDa 
  • Atom Count: 5,400 
  • Modeled Residue Count: 696 
  • Deposited Residue Count: 1,113 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab heavy chain225Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab light chain217Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C-C chemokine receptor type 8, Green fluorescent protein fusion671Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: CCR8GFP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P51685 (Homo sapiens)
Explore P51685 
Go to UniProtKB:  P51685
PHAROS:  P51685
GTEx:  ENSG00000179934 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P51685
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary