3X3F | pdb_00003x3f

TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2

• PDB DOI: https://doi.org/10.2210/pdb3X3F/pdb

• Classification: APOPTOSIS/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2015-01-20 Released: 2015-12-23 
• Deposition Author(s): Tamada, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Models: experimental

Literature

TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2

Tamada, T., Shinmi, D., Ikeda, M., Yonezawa, Y., Kataoka, S., Kuroki, R., Mori, E., Motoki, K.

(2015) Sci Rep 5: 17936-17936

• PubMed: 26672965 
• DOI: https://doi.org/10.1038/srep17936
• Primary Citation Related Structures: 
  3X3F, 3X3G


• PubMed Abstract: 
  

  The fully human monoclonal antibody KMTR2 acts as a strong direct agonist for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor 2 (TRAIL-R2), which is capable of inducing apoptotic cell death without cross-linking. To investigate the mechanism of direct agonistic activity induced by KMTR2, the crystal structure of the extracellular region of TRAIL-R2 and a Fab fragment derived from KMTR2 (KMTR2-Fab) was determined to 2.1 Å resolution. Two KMTR2-Fabs assembled with the complementarity-determining region 2 of the light chain via two-fold crystallographic symmetry, suggesting that the KMTR2-Fab assembly tended to enhance TRAIL-R2 oligomerization. A single mutation at Asn53 to Arg located at the two-fold interface in the KMTR2 resulted in a loss of its apoptotic activity, although it retained its antigen-binding activity. These results indicate that the strong agonistic activity, such as apoptotic signaling and tumor regression, induced by KMTR2 is attributed to TRAIL-R2 superoligomerization induced by the interdimerization of KMTR2.

---

Organizational Affiliation: 
• Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4, Shirakata, Tokai, Ibaraki 319-1195, Japan.
Research Core Function Laboratories, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida, Tokyo, 194-8533, Japan.
Immunology &Allergy Research Laboratories, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida, Tokyo, 194-8533, Japan.
Business Development Department, Kyowa Hakko Kirin Co., Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo, 100-8185, Japan.
R&D Planning Department, R&D Division, Kyowa Hakko Kirin Co., Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo, 100-8185, Japan.
Oncology Research Laboratories, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida, Tokyo, 194-8533, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.94 kDa 
• Atom Count: 4,199 
• Modeled Residue Count: 507 
• Deposited Residue Count: 585 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of KMTR2	A [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of KMTR2	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 10B	C [auth A]	142	Homo sapiens	Mutation(s): 0  Gene Names: DR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9
UniProt & NIH Common Fund Data Resources
Find proteins for O14763 (Homo sapiens) Explore O14763  Go to UniProtKB:  O14763
PHAROS:  O14763 GTEx:  ENSG00000120889

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth L], G [auth L], H [auth L], I [auth L], J [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.974	α = 90
b = 151.563	β = 90
c = 65.044	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Tamada, T.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2015-12-30
  Changes: Derived calculations
• Version 1.2: 2018-10-17
  Changes: Data collection, Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-30
  Changes: Structure summary