4N90 | pdb_00004n90

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

• PDB DOI: https://doi.org/10.2210/pdb4N90/pdb

• Classification: Apoptosis/Immune System
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-18 Released: 2014-09-03 
• Deposition Author(s): Huang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.286 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.229 (Depositor) 

Literature

Apo2L/TRAIL and the Death Receptor 5 Agonist Antibody AMG 655 Cooperate to Promote Receptor Clustering and Antitumor Activity.

Graves, J.D., Kordich, J.J., Huang, T.H., Piasecki, J., Bush, T.L., Sullivan, T., Foltz, I.N., Chang, W., Douangpanya, H., Dang, T., O'Neill, J.W., Mallari, R., Zhao, X., Branstetter, D.G., Rossi, J.M., Long, A.M., Huang, X., Holland, P.M.

(2014) Cancer Cell 26: 177-189

• PubMed: 25043603 
• DOI: https://doi.org/10.1016/j.ccr.2014.04.028
• Primary Citation Related Structures: 
  4N90


• PubMed Abstract: 
  

  Death receptor agonist therapies have exhibited limited clinical benefit to date. Investigations into why Apo2L/TRAIL and AMG 655 preclinical data were not predictive of clinical response revealed that coadministration of Apo2L/TRAIL with AMG 655 leads to increased antitumor activity in vitro and in vivo. The combination of Apo2L/TRAIL and AMG 655 results in enhanced signaling and can sensitize Apo2L/TRAIL-resistant cells. Structure determination of the Apo2L/TRAIL-DR5-AMG 655 ternary complex illustrates how higher order clustering of DR5 is achieved when both agents are combined. Enhanced agonism generated by combining Apo2L/TRAIL and AMG 655 provides insight into the limited efficacy observed in previous clinical trials and suggests testable hypotheses to reconsider death receptor agonism as a therapeutic strategy.

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Organizational Affiliation: 
• Department of Oncology Research, Amgen Inc., Seattle, WA 98119, USA.
Therapeutic Innovation Unit, Amgen Inc., Cambridge, MA 02142, USA.
Therapeutic Innovation Unit, Amgen Inc., Seattle, WA 98119, USA.
Department of Biologic Discovery, Amgen British Columbia, Burnaby, BC V5A 1V7, Canada.
Department of Clinical Immunology, Amgen Inc., South San Francisco, CA 94080, USA.
Department of Biologic Optimization, Amgen Inc., Seattle, WA 98119, USA.
Department of Molecular Structure and Characterization, Amgen, South San Francisco, CA, 94080, USA.
Department of Pathology, Amgen Inc., Seattle, WA 98119, USA.
Department of Molecular Sciences and Computational Biology, Amgen Inc., Thousand Oaks, CA 91320, USA.
Department of Molecular Structure and Characterization, Amgen Inc., Cambridge, MA 02142, USA.
Therapeutic Innovation Unit, Amgen Inc., Cambridge, MA 02142, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 242.78 kDa 
• Atom Count: 15,934 
• Modeled Residue Count: 2,074 
• Deposited Residue Count: 2,199 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 10B	A [auth R], B [auth S], C [auth T]	126	Homo sapiens	Mutation(s): 0  Gene Names: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186
UniProt & NIH Common Fund Data Resources
Find proteins for O14763 (Homo sapiens) Explore O14763  Go to UniProtKB:  O14763
PHAROS:  O14763 GTEx:  ENSG00000120889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 10	D [auth A], E [auth B], F [auth C]	168	Homo sapiens	Mutation(s): 0  Gene Names: TNFSF10, APO2L, TRAIL
UniProt & NIH Common Fund Data Resources
Find proteins for P50591 (Homo sapiens) Explore P50591  Go to UniProtKB:  P50591
PHAROS:  P50591 GTEx:  ENSG00000121858

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	G [auth E], I [auth G], K [auth I]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	H [auth D], J [auth F], L [auth H]	224	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.286 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.229 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.006	α = 90
b = 152.006	β = 90
c = 613.155	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Huang, X.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary