3X3F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/srep17936
  • Primary Citation of Related Structures:  

  • 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 investiga ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of KMTR2
H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain of KMTR2
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 10B
A
142Homo sapiensMutation(s): 0 
Gene Names: TNFRSF10B (DR5, KILLER, TRAILR2, TRICK2, ZTNFR9)
Find proteins for O14763 (Homo sapiens)
Go to Gene View: TNFRSF10B
Go to UniProtKB:  O14763
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 144.974α = 90.00
b = 151.563β = 90.00
c = 65.044γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-20 
  • 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
    Type: Derived calculations
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references