PDBsum entry: 1iqa

Cytokine

PDB id: 1iqa

Contents

Protein chains

156 a.a. *

Waters ×69

* Residue conservation analysis

PDB id:

1iqa

Name:

Cytokine

Title:

Crystal structure of the extracellular domain of mouse rank ligand

Structure:

Receptor activator of nuclear factor kappa b ligand. Chain: a, b, c. Fragment: extracellular domain (residues 157-316). Synonym: tumor necrosis factor ligand superfamily member 11, rankl, trance, opgl, odf. Engineered: yes. Mutation: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.20Å R-factor: 0.226 R-free: 0.274

Authors:

S.Ito,K.Wakabayashi,O.Ubukata,S.Hayashi,F.Okada,T.Hata

Key ref:

S.Ito et al. (2002). Crystal structure of the extracellular domain of mouse RANK ligand at 2.2-A resolution. J Biol Chem, 277, 6631-6636. PubMed id: 11733492 DOI: 10.1074/jbc.M106525200

Date:

11-Jul-01 Release date: 13-Mar-02

Protein chains

O35235  (TNF11_MOUSE) -  Tumor necrosis factor ligand superfamily member 11

Seq: 316 a.a.

Struc: 156 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: immune response (1 term)
• Biochemical function: tumor necrosis factor receptor binding (1 term)

DOI no: 10.1074/jbc.M106525200

J Biol Chem 277:6631-6636 (2002)

PubMed id: 11733492

Crystal structure of the extracellular domain of mouse RANK ligand at 2.2-A resolution.

S.Ito, K.Wakabayashi, O.Ubukata, S.Hayashi, F.Okada, T.Hata.

ABSTRACT

Bone remodeling involves the resorption of bone by osteoclasts and the synthesis of bone matrix by osteoblasts. Receptor activator of NF-kappa B ligand (RANKL, also known as ODF and OPGL), a member of the tumor necrosis factor (TNF) family, triggers osteoclastogenesis by forming a complex with its receptor, RANK. We have determined the crystal structure of the extracellular domain of mouse RANKL at 2.2-A resolution. The structure reveals that the RANKL extracellular domain is trimeric, which was also shown by analytical ultracentrifugation, and each subunit has a beta-strand jellyroll topology like the other members of the TNF family. A comparison of RANKL with TNF beta and TNF-related apoptosis-inducing ligand (TRAIL), whose structures were determined to be in the complex form with their respective receptor, reveals conserved and specific features of RANKL in the TNF superfamily and suggests the presence of key residues of RANKL for receptor binding.

Selected figure(s)

Figure 3.
Fig. 3. Mouse RANKL trimer and monomer. A, schematic view of the mouse RANKL trimer shown with strands as arrows and labeled by the notation of Eck and Sprang (12). The three monomers are depicted in different colors. In this orientation, the cell surface containing mouse RANKL is located at the bottom of the figure. B, stereoview of the superposition of the mouse RANKL, TNF , and TRAIL monomers. The superposition was carried out using the program O ( 29). The figure shows the C traces with mouse RANKL colored in red, TNF colored in blue, and TRAIL colored in green. The numbers indicate the N-terminal and C-terminal residues of mouse RANKL. The figures were prepared with the programs Molscript (36) and Raster3D (37).

Figure 6.
Fig. 6. Charge distribution for mouse RANKL, TNF , and TRAIL. A, surface representation of the mRANKL trimer with each monomer colored differently. B, ribbon drawing of the mRANKL monomer in the same orientation as that in A. The three key residues predicted to be important for receptor binding are shown as ball-and-stick models. C, blue and red denote positive and negative charges, respectively. The orientation is the same as that of A and B. The figures were prepared with Insight II (Molecular Simulations Inc.).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 6631-6636) copyright 2002.

Figures were selected by an automated process.