PDBsum entry 2fbo

Immune system

PDB id: 2fbo

Contents

Protein chain

250 a.a. *

Waters ×277

* Residue conservation analysis

PDB id:

2fbo

Name:

Immune system

Title:

Crystal structure of the two tandem v-type regions of vcbp3 (v-region- containing chitin binding protein) to 1.85 a

Structure:

Variable region-containing chitin-binding protein 3. Chain: j. Synonym: vcbp3 tandem v regions. V1v2. Engineered: yes

Source:

Branchiostoma floridae. Florida lancelet. Organism_taxid: 7739. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.85Å R-factor: 0.228 R-free: 0.269

Authors:

J.A.Hernandez Prada,R.N.Haire,J.Jakoncic,J.P.Cannon,G.W.Litman, D.A.Ostrov

Key ref:

J.A.Hernández Prada et al. (2006). Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus. Nat Immunol, 7, 875-882. PubMed id: 16799561 DOI: 10.1038/ni1359

Date:

09-Dec-05 Release date: 17-Oct-06

Protein chain

Q8I9N0  (Q8I9N0_BRAFL) -  chitinase from Branchiostoma floridae

Seq: 334 a.a.

Struc: 250 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.14 - chitinase.
• Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.

DOI no: 10.1038/ni1359

Nat Immunol 7:875-882 (2006)

PubMed id: 16799561

Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus.

J.A.Hernández Prada, R.N.Haire, M.Allaire, J.Jakoncic, V.Stojanoff, J.P.Cannon, G.W.Litman, D.A.Ostrov.

ABSTRACT

Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region-containing chitin-binding proteins (VCBPs) are diversified immune-type molecules found in amphioxus (Branchiostoma floridae), an invertebrate that diverged early in deuterostome phylogeny. To study the potential evolutionary relationships between VCBPs and vertebrate adaptive immune receptors, we solved the structures of both a single V-type domain (to 1.15 A) and a pair of V-type domains (to 1.85 A) from VCBP3. The deduced structures show integral features of the ancestral variable-region fold as well as unique features of variable-region pairing in molecules that may reflect characteristics of ancestral forms of diversified immune receptors found in modern-day vertebrates.

Selected figure(s)

Figure 1.
Figure 1. Structural comparison of the VCBP3 domain fold and packing interactions with antigen receptors. (a) Among V-set immunoglobulin domains, VCBP3 V1 is most similar to a TCR V[ ]domain (in salmon superimposed on V1, in cyan); the CC' loop is curled over the front sheet (A'GFCC'C") in V1. (b) VCBP3 V1 (cyan) superimposed on V2 (gold). The FG loops and G strands, encoded by J region–like elements in VCBPs, are nearly identical, whereas the BC and CC' loops of V1 are longer than those in V2.

Figure 5.
Figure 5. Crystal structure of VCBP3 V1 V2 solved by single-wavelength anomalous dispersion and refined to 1.85 Å. (a,b) Secondary structure ( -strands, gold; loop regions, gray; helices, red). The G strand and FG loop encoded by a J gene segment–like element is cyan. Loops corresponding to CDR regions in TCR and immunoglobulin: BC loop, CDR1; C'C", CDR2; FG, CDR3. (c,d) The molecular surface of VCBP3 V1 V2. The molecular surface of V1 is magenta and that of V2 is violet. Polymorphic residues in VCBP sequences (gold) form a contiguous patch of solvent-exposed hypervariable residues (outlined by a green dashed rectangle). The views in b,d are rotated 180° about a vertical axis in plane of the page with respect to a,c.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Immunol (2006, 7, 875-882) copyright 2006.

Figures were selected by an automated process.