Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 102398.38 
• Atom Count: 6292 
• Residue Count: 894 
• Unique protein chains: 2

1D0G

CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL

• DOI: 10.2210/pdb1D0G/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus, Bacteria


• Deposited: 1999-09-09 Released: 1999-10-22 
• Deposition Author(s): Hymowitz, S.G., Christinger, H.W., Fuh, G., O'Connell, M.P., Kelley, R.F., Ashkenazi, A., de Vos, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.267 
• R-Value Work: 0.222 

Literature

Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5.

Hymowitz, S.G., Christinger, H.W., Fuh, G., Ultsch, M., O'Connell, M., Kelley, R.F., Ashkenazi, A., de Vos, A.M.

(1999) Mol.Cell 4: 563-571

• PubMed: 10549288 


• PubMed Abstract: 
  

Formation of a complex between Apo2L (also called TRAIL) and its signaling receptors, DR4 and DR5, triggers apoptosis by inducing the oligomerization of intracellular death domains. We report the crystal structure of the complex between Apo2L and the ectodomain of DR5. The structure shows three elongated receptors snuggled into long crevices between pairs of monomers of the homotrimeric ligand. The interface is divided into two distinct patches, one near the bottom of the complex close to the receptor cell surface and one near the top. Both patches contain residues that are critical for high-affinity binding. A comparison to the structure of the lymphotoxin-receptor complex suggests general principles of binding and specificity for ligand recognition in the TNF receptor superfamily.

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Organizational Affiliation: 

Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DEATH RECEPTOR-5	R, S, T	130	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
APOPTOSIS-2 LIGAND	A, B, D	168	Homo sapiens	Mutation(s): 0  Gene Names: TNFSF10 (APO2L, TRAIL)
Find proteins for P50591 (Homo sapiens) Go to Gene View: TNFSF10 Go to UniProtKB:  P50591

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.267 
• R-Value Work: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 66.818	α = 90.00
b = 111.019	β = 90.00
c = 130.807	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	refinement
AMoRE	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-09 
• Released Date: 1999-10-22 
• Deposition Author(s): Hymowitz, S.G., Christinger, H.W., Fuh, G., O'Connell, M.P., Kelley, R.F., Ashkenazi, A., de Vos, A.M.

Revision History 

• Version 1.0: 1999-10-22
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Advisory, Experimental preparation