6BWV

Crystal Structure of the 4-1BB/4-1BBL Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of the human 4-1BB/4-1BBL complex.

Gilbreth, R.N., Oganesyan, V.Y., Amdouni, H., Novarra, S., Grinberg, L., Barnes, A., Baca, M.

(2018) J Biol Chem 293: 9880-9891

  • DOI: 10.1074/jbc.RA118.002803
  • Primary Citation of Related Structures:  
    6BWV

  • PubMed Abstract: 

    • 4-1BBL is a member of the tumor necrosis factor (TNF) superfamily and is the ligand for the TNFR superfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells, and agonists of this receptor have garnered strong attention as potential immunotherapy agents ...

    4-1BBL is a member of the tumor necrosis factor (TNF) superfamily and is the ligand for the TNFR superfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells, and agonists of this receptor have garnered strong attention as potential immunotherapy agents. Broadly speaking, the structural features of TNF superfamily members, their receptors, and ligand-receptor complexes are similar. However, a published crystal structure of human 4-1BBL suggests that it may be unique in this regard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4-Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly.

    Organizational Affiliation: 

    From the Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, Maryland 20878 Manuel.Baca@gilead.com.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 9 A, B156Homo sapiensMutation(s): 0 
Gene Names: TNFSF9
Find proteins for P41273 (Homo sapiens)
Explore P41273 
Go to UniProtKB:  P41273
NIH Common Fund Data Resources
PHAROS:  P41273
GTEx:  ENSG00000125657
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9 D, E141Homo sapiensMutation(s): 3 
Gene Names: TNFRSF9, CD137, ILA
Find proteins for Q07011 (Homo sapiens)
Explore Q07011 
Go to UniProtKB:  Q07011
NIH Common Fund Data Resources
PHAROS:  Q07011
GTEx:  ENSG00000049249
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.571α = 90
b = 161.571β = 90
c = 161.571γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references