2X29 | pdb_00002x29

Crystal structure of human4-1BB ligand ectodomain

• PDB DOI: https://doi.org/10.2210/pdb2X29/pdb
• Entry: 2X29 supersedes: 2WAK

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-12 Released: 2010-03-23 
• Deposition Author(s): Won, E.Y., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

The Structure of the Trimer of Human 4-1Bb Ligand is Unique Among Members of the Tumor Necrosis Factor Superfamily.

Won, E.Y., Cha, K., Byun, J.S., Kim, D.U., Shin, S., Ahn, B., Kim, Y.H., Rice, A.J., Walz, T., Kwon, B.S., Cho, H.S.

(2010) J Biological Chem 285: 9202

• PubMed: 20032458 
• DOI: https://doi.org/10.1074/jbc.M109.084442
• Primary Citation Related Structures: 
  2X29


• PubMed Abstract: 
  

  Binding of the 4-1BB ligand (4-1BBL) to its receptor, 4-1BB, provides the T lymphocyte with co-stimulatory signals for survival, proliferation, and differentiation. Importantly, the 4-1BB-4-1BBL pathway is a well known target for anti-cancer immunotherapy. Here we present the 2.3-A crystal structure of the extracellular domain of human 4-1BBL. The ectodomain forms a homotrimer with an extended, three-bladed propeller structure that differs from trimers formed by other members of the tumor necrosis factor (TNF) superfamily. Based on the 4-1BBL structure, we modeled its complex with 4-1BB, which was consistent with images obtained by electron microscopy, and verified the binding site by site-directed mutagenesis. This structural information will facilitate the development of immunotherapeutics targeting 4-1BB.

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Organizational Affiliation: 
• Department of Biology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul 120-749, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 17.82 kDa 
• Atom Count: 1,247 
• Modeled Residue Count: 156 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9	A	167	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P41273 (Homo sapiens) Explore P41273  Go to UniProtKB:  P41273
PHAROS:  P41273 GTEx:  ENSG00000125657

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.846	α = 90
b = 121.846	β = 90
c = 33.575	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Won, E.Y., Cho, H.S.
• This entry supersedes: 2WAK

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary