PDBsum entry 1vex

Cell adhesion

PDB id: 1vex

Contents

Protein chain

56 a.a. *

* Residue conservation analysis

PDB id:

1vex

Name:

Cell adhesion

Title:

F-spondin tsr domain 4

Structure:

F-spondin. Chain: a. Fragment: f-spondin tsr domain 4. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

20 models

Authors:

K.Paakkonen,H.Tossavainen,P.Permi,I.Kilpelainen,P.Guntert

Key ref:

K.Pääkkönen et al. (2006). Solution structures of the first and fourth TSR domains of F-spondin. Proteins, 64, 665-672. PubMed id: 16736493 DOI: 10.1002/prot.21030

Date:

06-Apr-04 Release date: 19-Apr-05

Protein chain

P35446  (SPON1_RAT) -  Spondin-1 from Rattus norvegicus

Seq: 807 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1002/prot.21030

Proteins 64:665-672 (2006)

PubMed id: 16736493

Solution structures of the first and fourth TSR domains of F-spondin.

K.Pääkkönen, H.Tossavainen, P.Permi, H.Rakkolainen, H.Rauvala, E.Raulo, I.Kilpeläinen, P.Güntert.

ABSTRACT

F-spondin is a protein mainly associated with neuronal development. It attaches to the extracellular matrix and acts in the axon guidance of the developing nervous system. F-spondin consists of eight domains, six of which are TSR domains. The TSR domain family binds a wide range of targets. Here we present the NMR solution structures of TSR1 and TSR4. TSR domains have an unusual fold that is characterized by a long, nonglobular shape, consisting of two beta-strands and one irregular extended strand. Three disulfide bridges and stack of alternating tryptophan and arginine side-chains stabilize the structure. TSR1 and TSR4 structures are similar to each other and to the previously determined TSR domain X-ray structures from another protein, TSP, although TSR4 exhibits a mobile loop not seen in other structures.

Selected figure(s)

Figure 1.
Figure 1. The NMR solution of structures of (A) the F-spondin TSR domain 1 and (B) the F-spondin TSR domain 4. Twenty energy-refined conformers are shown for each domain. The first strand has a rippled conformation, which is characteristic for this fold. The two other strands form an antiparallel -sheet (residues 462-467 and 484-489 for TSR1, and 634-640 and 657-663 for TSR4). TSR1 has a short additional -sheet in the region where TSR4 has a less well-defined loop region (residues 443-445 and 471-473). The secondary structure and core residues of a representative conformer of the solution structures of the F-spondin (C) TSR1 and (D) TSR4 domains are shown. Tryptophans are drawn in blue, arginines in red, and cysteines in yellow. The green residue in TSR1 is tyrosine, which may further stabilize the structure through interactions with the nearby arginine side-chain. In TSR4, this residue is leucine. Aspartate 485 is shown in magenta.

Figure 4.
Figure 4. Electrostatic surface potentials of (A) TSP TSR2, (B) F-spondin TSR1, and (C) F-spondin TSR4. Each domain is shown from two sides, which are rotated by 180° around a vertical axis relative to each other. For the F-spondin TSR domains, the structures with the lowest total energy are shown. Charged residues are labeled. Red labels identify residues that are conserved in the sequence alignment and have similar positions on the surfaces of all three domains. The charged side-chains D496, E497, and D498 in F-spondin TSR1 and D625, K632, K642, E646, D649, and D653 in F-spondin TSR4 have larger than 2 Å side-chain RMSDs.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 64, 665-672) copyright 2006.

Figures were selected by the author.