Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 51335.49 
• Atom Count: 3344 
• Residue Count: 471 
• Unique protein chains: 1

2ZJC

TNFR1 selectve TNF mutant; R1-6

• DOI: 10.2210/pdb2ZJC/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 11 


• Deposited: 2008-03-05 Released: 2009-01-20 
• Deposition Author(s): Mukai, Y., Yamagata, Y., Tsutsumi, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.272 
• R-Value Work: 0.201 

Literature

Structure-Function Relationship of Tumor Necrosis Factor (TNF) and Its Receptor Interaction Based on 3D Structural Analysis of a Fully Active TNFR1-Selective TNF Mutant

Mukai, Y., Shibata, H., Nakamura, T., Yoshioka, Y., Abe, Y., Nomura, T., Taniai, M., Ohta, T., Ikemizu, S., Nakagawa, S., Tsunoda, S., Kamada, H., Yamagata, Y., Tsutsumi, Y.

(2009) J.Mol.Biol. 385: 1221-1229

• PubMed: 19084540 
• DOI: 10.1016/j.jmb.2008.11.053


• PubMed Abstract: 
  

Tumor necrosis factor (TNF) is an important cytokine that suppresses carcinogenesis and excludes infectious pathogens to maintain homeostasis. TNF activates its two receptors [TNF receptor (TNFR) 1 and TNFR2], but the contribution of each receptor to various host defense functions and immunologic surveillance is not yet clear. Here, we used phage display techniques to generate receptor-selective TNF mutants that activate only one TNFR. These TNF mutants will be useful in the functional analysis of TNFR. Six amino acids in the receptor binding interface (near TNF residues 30, 80, and 140) were randomly mutated by polymerase chain reaction. Two phage libraries comprising over 5 million TNF mutants were constructed. By selecting the mutants without affinity for TNFR1 or TNFR2, we successfully isolated 4 TNFR2-selective candidates and 16 TNFR1-selective candidates, respectively. The TNFR1-selective candidates were highly mutated near residue 30, whereas TNFR2-selective candidates were highly mutated near residue 140, although both had conserved sequences near residues 140 and 30, respectively. This finding suggested that the phage display technique was suitable for identifying important regions for the TNF interaction with TNFR1 and TNFR2. Purified clone R1-6, a TNFR1-selective candidate, remained fully bioactive and had full affinity for TNFR1 without activating TNFR2, indicating the usefulness of the R1-6 TNF mutant in analyzing TNFR1 receptor function. To further elucidate the receptor selectivity of R1-6, we examined the structure of R1-6 by X-ray crystallography. The results suggested that R31A and R32G mutations strongly influenced electrostatic interaction with TNFR2, and that L29K mutation contributed to the binding of R1-6 to TNFR1. This phage display technique can be used to efficiently construct functional mutants for analysis of the TNF structure-function relationship, which might facilitate in silico drug design based on receptor selectivity.

---

Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tumor necrosis factor	A, B, C	157	Homo sapiens	Mutation(s): 11  Gene Names: TNF (TNFA, TNFSF2)
Find proteins for P01375 (Homo sapiens) Go to Gene View: TNF Go to UniProtKB:  P01375

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.272 
• R-Value Work: 0.201 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 135.873	α = 90.00
b = 135.873	β = 90.00
c = 58.023	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-05 
• Released Date: 2009-01-20 
• Deposition Author(s): Mukai, Y., Yamagata, Y., Tsutsumi, Y.

Revision History 

• Version 1.0: 2009-01-20
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance