5CIR | pdb_00005cir

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

• PDB DOI: https://doi.org/10.2210/pdb5CIR/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-07-13 Released: 2017-01-18 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Models: experimental

Literature

The structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex.

Ramamurthy, V., Yamniuk, A.P., Lawrence, E.J., Yong, W., Schneeweis, L.A., Cheng, L., Murdock, M., Corbett, M.J., Doyle, M.L., Sheriff, S.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1273-1281

• PubMed: 26457518 
• DOI: https://doi.org/10.1107/S2053230X15016416
• Primary Citation Related Structures: 
  5CIR


• PubMed Abstract: 
  

  The structure of death receptor 4 (DR4) in complex with TNF-related apoptosis-inducing ligand (TRAIL) has been determined at 3 Å resolution and compared with those of previously determined DR5-TRAIL complexes. Consistent with the high sequence similarity between DR4 and DR5, the overall arrangement of the DR4-TRAIL complex does not differ substantially from that of the DR5-TRAIL complex. However, subtle differences are apparent. In addition, solution interaction studies were carried out that show differences in the thermodynamics of binding DR4 or DR5 with TRAIL.

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Organizational Affiliation: 
• Molecular Structure and Design, Bristol-Myers Squibb R&D, PO Box 4000, Princeton, NJ 08543-4000, USA.
Protein Science, Bristol-Myers Squibb R&D, PO Box 4000, Princeton, NJ 08543-4000, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 94.3 kDa 
• Atom Count: 5,611 
• Modeled Residue Count: 752 
• Deposited Residue Count: 831 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 10	A, B, C [auth D]	169	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 10A	D [auth E], E [auth F], F [auth G]	108	Homo sapiens	Mutation(s): 2  Gene Names: TNFRSF10A, APO2, DR4, TRAILR1
UniProt & NIH Common Fund Data Resources
Find proteins for O00220 (Homo sapiens) Explore O00220  Go to UniProtKB:  O00220
PHAROS:  O00220 GTEx:  ENSG00000104689

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.216 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.6	α = 90
b = 87.6	β = 90
c = 107.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary