6CU0

Crystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

Starting Models: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier.

Bitra, A.Doukov, T.Croft, M.Zajonc, D.M.

(2018) J Biol Chem 293: 9958-9969

  • DOI: https://doi.org/10.1074/jbc.RA118.003176
  • Primary Citation of Related Structures:  
    6CPR, 6CU0, 6D3N

  • PubMed Abstract: 

    Human (h)4-1BB (TNFRSF9 or CD137) is an inducible tumor necrosis factor receptor (TNFR) superfamily member that interacts with its cognate ligand h4-1BBL to promote T lymphocyte activation and proliferation. h4-1BB is currently being targeted with agonists in cancer immunotherapy. Here, we determined the crystal structures of unbound h4-1BBL and both WT h4-1BB and a dimerization-deficient h4-1BB mutant (C121S) in complex with h4-1BBL at resolutions between 2.7 and 3.2 Å. We observed that the structural arrangement of 4-1BBL, both unbound and in the complex, represents the canonical bell shape as seen in other similar TNF proteins and differs from the previously reported three-bladed propeller structure of 4-1BBL. We also found that the binding site for the receptor is at the crevice formed between two protomers of h4-1BBL, but that h4-1BB interacts predominantly with only one ligand protomer. Moreover, h4-1BBL lacked the conserved tyrosine residue in the DE loop that forms canonical interactions between other TNFR family molecules and their ligands, suggesting h4-1BBL engages h4-1BB through a distinct mechanism. Of note, we discovered that h4-1BB forms a disulfide-linked dimer because of the presence of an additional cysteine residue found in its cysteine-rich domain 4 (CRD4). As a result, h4-1BB dimerization, in addition to trimerization via h4-1BBL binding, could result in cross-linking of individual ligand-receptor complexes to form a 2D network that stimulates strong h4-1BB signaling. This work provides critical insights into the structural and functional properties of both h4-1BB and h4-1BBL and reveals that covalent receptor dimerization amplifies h4-1BB signaling.


  • Organizational Affiliation

    From the Division of Immune Regulation, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California 92037.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 9
A, B, C, D, E
A, B, C, D, E, F
165Homo sapiensMutation(s): 0 
Gene Names: TNFSF9
UniProt & NIH Common Fund Data Resources
Find proteins for P41273 (Homo sapiens)
Explore P41273 
Go to UniProtKB:  P41273
PHAROS:  P41273
GTEx:  ENSG00000125657 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41273
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9138Homo sapiensMutation(s): 1 
Gene Names: TNFRSF9CD137ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens)
Explore Q07011 
Go to UniProtKB:  Q07011
PHAROS:  Q07011
GTEx:  ENSG00000049249 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07011
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q07011-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.961α = 90
b = 114.745β = 101.24
c = 126.039γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Structure summary