PDBsum entry 1ext

Signalling protein

PDB id: 1ext

Contents

Protein chain

160 a.a. *

Ligands

SO4 ×3

Metals

_MG

Waters ×400

* Residue conservation analysis

PDB id:

1ext

Name:

Signalling protein

Title:

Extracellular domain of the 55kda tumor necrosis factor receptor. Crystallized at ph3.7 in p 21 21 21.

Structure:

Tumor necrosis factor receptor. Chain: a, b. Fragment: extracellular domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the construct contains residues 12 to 172 of the mature sequence of the entire receptor. Residue 11 is mutated to met as a result of the expression system

Biol. unit:

Dimer (from PQS)

Resolution:

1.85Å R-factor: 0.203 R-free: 0.243

Authors:

J.H.Naismith,S.R.Sprang

Key ref:

J.H.Naismith et al. (1996). Structures of the extracellular domain of the type I tumor necrosis factor receptor. Structure, 4, 1251-1262. PubMed id: 8939750 DOI: 10.1016/S0969-2126(96)00134-7

Date:

03-Jul-96 Release date: 11-Jan-97

Protein chains

P19438  (TNR1A_HUMAN) -  Tumor necrosis factor receptor superfamily member 1A from Homo sapiens

Seq: 455 a.a.

Struc: 160 a.a.

DOI no: 10.1016/S0969-2126(96)00134-7

Structure 4:1251-1262 (1996)

PubMed id: 8939750

Structures of the extracellular domain of the type I tumor necrosis factor receptor.

J.H.Naismith, T.Q.Devine, T.Kohno, S.R.Sprang.

ABSTRACT

BACKGROUND: Tumor necrosis factor (TNF) is a powerful cytokine that is involved in immune and pro-inflammatory responses. Two TNF receptors that belong to the cysteine-rich low affinity nerve growth factor receptor family (TNF-R1 and TNF-R2) are the sole mediators of TNF signalling. Signalling is thought to occur when a trimer of TNF binds to the extracellular domains of two or three receptor molecules, which permits aggregation and activation of the cytoplasmic domains. The complex is then internalized within an endocytic vesicle, whereupon it dissociates at low pH. Structure of the soluble extracellular domain of the receptor (sTNF-R1) both in the unliganded and TNF-bound state have previously been determined. In both instances, the fourth subdomain of the receptor was found to be partly disordered. In the unliganded state at pH 7.5, the extracellular domain forms two distinct types of dimer, parallel and antiparallel; the antiparallel dimer occludes the TNF-binding. RESULTS: We have determined the structure of sTNF-R1 in two crystal forms in high salt at pH 3.7. The orthorhombic crystals diffract to 1.85 ånd the entire polypeptide is well ordered. In contrast, the C-terminal 32 residues are disordered in the hexagonal crystals. In the orthorhombic form, these residues exhibit a topology and disulphide connectivity that differs from the other three cysteine-rich domains in the molecule. In both forms, the interface is considerably more extensive than that used in complex formation with LTalpha. This 'low pH' dimer is different from both of the dimers observed in crystals grown at pH 7.5. CONCLUSIONS: The occurrence of the antiparallel dimers in both low pH crystal forms suggest that they are not an artefact of crystal packing. Such dimers may form in the low pH environment of the endosome. Because the dimer contact surface occludes the TNF-binding site, formation of this dimer would dissociate the TNF-receptor complex within the endosome. Three of the four cysteine-rich domains of TNF-R1 are constructed from two distinct structural modules, termed A1 and B2. The fourth subdomain comprises an A1 module followed by an unusual C2 module. Although the orientation of these modules with respect to each other is sensitive to crystal packing, ligand binding, pH and ionic strength, the modules are structurally well conserved between and within the known sTNF-R1 structures.

Selected figure(s)

Figure 1.
Figure 1. The complete structure of the monomer of sTNF-R1. (a) A stereo diagram of the numbered Cα trace of the sTNF-R1 molecule found at pH 3.7. (b) A ribbon representation of the structure with disulphide bonds shown as yellow spheres, prepared with RASTER3D [31]. Subdomains one and three are in red and subdomains two and four in orange. Figure 1. The complete structure of the monomer of sTNF-R1. (a) A stereo diagram of the numbered Cα trace of the sTNF-R1 molecule found at pH 3.7. (b) A ribbon representation of the structure with disulphide bonds shown as yellow spheres, prepared with RASTER3D [[4]31]. Subdomains one and three are in red and subdomains two and four in orange.

Figure 3.
Figure 3. Two orthogonal views of the low pH dimer that is the asymmetric unit of the P2[1]2[1]2[1] crystal form. Careful examination of the figure shows that the interaction between subdomain one and subdomain four is closer at one end of the dimer than the other. (Figure prepared using RASTER3D [31].) The color scheme for one monomer is the same as in Figure 1. The other monomer is colored dark blue (subdomains one and three) and bright blue (subdomains two and four). Figure 3. Two orthogonal views of the low pH dimer that is the asymmetric unit of the P2[1]2[1]2[1] crystal form. Careful examination of the figure shows that the interaction between subdomain one and subdomain four is closer at one end of the dimer than the other. (Figure prepared using RASTER3D [[3]31].) The color scheme for one monomer is the same as in [4]Figure 1. The other monomer is colored dark blue (subdomains one and three) and bright blue (subdomains two and four).

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 1251-1262) copyright 1996.

Figures were selected by an automated process.