Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 66380.23 
• Atom Count: 3329 
• Residue Count: 621 
• Unique protein chains: 1

6MGE

Structure of human 4-1BBL

• DOI: 10.2210/pdb6MGE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni


• Deposited: 2018-09-13 Released: 2018-11-21 
• Deposition Author(s): Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Xu, A., Yang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 

Literature

Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab.

Chin, S.M., Kimberlin, C.R., Roe-Zurz, Z., Zhang, P., Xu, A., Liao-Chan, S., Sen, D., Nager, A.R., Oakdale, N.S., Brown, C., Wang, F., Yang, Y., Lindquist, K., Yeung, Y.A., Salek-Ardakani, S., Chaparro-Riggers, J.

(2018) Nat Commun 9: 4679-4679

• PubMed: 30410017 
• DOI: 10.1038/s41467-018-07136-7
• Primary Citation of Related Structures:  
  6MHR, 6MI2


• PubMed Abstract: 
  

4-1BB (CD137, TNFRSF9) is an inducible costimulatory receptor expressed on activated T cells. Clinical trials of two agonist antibodies, utomilumab (PF-05082566) and urelumab (BMS-663513), are ongoing in multiple cancer indications, and both antibodies demonstrate distinct activities in the clinic. To understand these differences, we solved structures of the human 4-1BB/4-1BBL complex, the 4-1BBL trimer alone, and 4-1BB bound to utomilumab or urelumab. The 4-1BB/4-1BBL complex displays a unique interaction between receptor and ligand when compared with other TNF family members. Furthermore, our ligand-only structure differs from previously published data. Utomilumab, a ligand-blocking antibody, binds 4-1BB between CRDs 3 and 4. In contrast, urelumab binds 4-1BB CRD-1, away from the ligand binding site. Finally, cell-based assays demonstrate utomilumab is a milder agonist than urelumab. Collectively, our data provide a deeper understanding of the 4-1BB signaling complex, providing a template for future development of next generation 4-1BB targeted biologics.

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Organizational Affiliation: 

Cancer Immunology Discovery, Pfizer Inc., 230 E. Grand Ave, South San Francisco, CA, 94080, USA. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tumor necrosis factor ligand superfamily member 9	A, B, C	207	Homo sapiens	Mutation(s): 0  Gene Names: TNFSF9
Find proteins for P41273 (Homo sapiens) Go to Gene View: TNFSF9 Go to UniProtKB:  P41273

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• Space Group: P 6₂

Unit Cell:

Length (Å)	Angle (°)
a = 118.910	α = 90.00
b = 118.910	β = 90.00
c = 105.494	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-13 
• Released Date: 2018-11-21 
• Deposition Author(s): Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Xu, A., Yang, Y.

Revision History 

• Version 1.0: 2018-11-21
  Type: Initial release