PDBsum entry 1kd7

Membrane protein

PDB id: 1kd7

Contents

Protein chains

(+ 0 more) 144 a.a. *

* Residue conservation analysis

PDB id:

1kd7

Name:

Membrane protein

Title:

Crystal structure of an extracellular domain fragment of human baff

Structure:

Tumor necrosis factor ligand superfamily member 13b. Chain: a, b, c, k, l, m. Fragment: extracellular domain fragment. Synonym: baff, tall-1, tnf-and-apol-related leukocyte expressed ligand 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922

Biol. unit:

Hexamer (from PQS)

Resolution:

2.80Å R-factor: 0.217 R-free: 0.250

Authors:

M.Karpusas,T.G.Cachero,F.Qian,A.Boriack-Sjodin,C.Mullen,K.Strauch,Y.- M.Hsu,S.L.Kalled

Key ref:

M.Karpusas et al. (2002). Crystal structure of extracellular human BAFF, a TNF family member that stimulates B lymphocytes. J Mol Biol, 315, 1145-1154. PubMed id: 11827482 DOI: 10.1006/jmbi.2001.5296

Date:

12-Nov-01 Release date: 12-Nov-02

Protein chains

Q9Y275  (TN13B_HUMAN) -  Tumor necrosis factor ligand superfamily member 13B from Homo sapiens

Seq: 285 a.a.

Struc: 144 a.a.

DOI no: 10.1006/jmbi.2001.5296

J Mol Biol 315:1145-1154 (2002)

PubMed id: 11827482

Crystal structure of extracellular human BAFF, a TNF family member that stimulates B lymphocytes.

M.Karpusas, T.G.Cachero, F.Qian, A.Boriack-Sjodin, C.Mullen, K.Strauch, Y.M.Hsu, S.L.Kalled.

ABSTRACT

B cell activating factor (BAFF), a ligand belonging to the tumor necrosis factor (TNF) family, plays a critical role in regulating survival and activation of peripheral B cell populations and has been associated with autoimmune disease. BAFF is known to interact with three receptors, BCMA, TACI and BAFF-R, that have distant similarities with other receptors of the TNF family. We have determined the crystal structure of the TNF-homologous domain of BAFF at 2.8 A resolution. The structure reveals significant differences when compared to other TNF family members, including an unusually long D-E loop that participates in the formation of a deep, concave and negatively charged region in the putative receptor binding site. The BAFF structure was further used to generate a homology model of APRIL, a closely related TNF family ligand that also binds to BCMA and TACI, but not BAFF-R. Analysis of the putative receptor binding sites of BAFF and APRIL suggests that differences in the D-E loop structure and electrostatic surface potentials may be important for determining binding specificities for BCMA, TACI and BAFF-R.

Selected figure(s)

Figure 1.
Figure 1. Representative region of the final 2F[o] - F[c] electron density map contoured at 1.0 s.

Figure 2.
Figure 2. Crystal structure of human BAFF. (a) BAFF trimer in ribbon representation. Monomers are colored differently and b-strands and N and C-terminal residues are labeled for the green-colored monomer. Also shown in the ball-and-stick representation are the disulfide bridge in red and the glycosylation site Asn242 in turquoise. (b) Space-filling model of BAFF viewed along the 3-fold axis from the top of the trimer. The arrows point to the putative receptor binding sites. The Figure was made with RIBBONS.[47]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 1145-1154) copyright 2002.

Figures were selected by an automated process.