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PDBsum entry 1vex

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protein links
Cell adhesion PDB id
1vex
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35446  (SPON1_RAT) -  Spondin-1
Seq:
Struc:
 
Seq:
Struc:
807 a.a.
56 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19752215 E.F.Ozdowski, Y.M.Mowery, and C.Cronmiller (2009).
Stall encodes an ADAMTS metalloprotease and interacts genetically with Delta in Drosophila ovarian follicle formation.
  Genetics, 183, 1027-1040.  
19424823 K.P.Holbourn, B.Perbal, and K.Ravi Acharya (2009).
Proteins on the catwalk: modelling the structural domains of the CCN family of proteins.
  J Cell Commun Signal, 3, 25-41.  
19894979 N.Rawat, and P.Biswas (2009).
Size, shape, and flexibility of proteins and DNA.
  J Chem Phys, 131, 165104.  
19153605 Y.Li, C.Cao, W.Jia, L.Yu, M.Mo, Q.Wang, Y.Huang, J.M.Lim, M.Ishihara, L.Wells, P.Azadi, H.Robinson, Y.W.He, L.Zhang, and R.A.Mariuzza (2009).
Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule.
  EMBO J, 28, 286-297.
PDB code: 3d34
18070664 B.J.Mans, J.F.Andersen, I.M.Francischetti, J.G.Valenzuela, T.G.Schwan, V.M.Pham, M.K.Garfield, C.H.Hammer, and J.M.Ribeiro (2008).
Comparative sialomics between hard and soft ticks: implications for the evolution of blood-feeding behavior.
  Insect Biochem Mol Biol, 38, 42-58.  
18789696 K.P.Holbourn, K.R.Acharya, and B.Perbal (2008).
The CCN family of proteins: structure-function relationships.
  Trends Biochem Sci, 33, 461-473.  
18602404 K.Tan, M.Duquette, J.H.Liu, J.Lawler, and J.H.Wang (2008).
The crystal structure of the heparin-binding reelin-N domain of f-spondin.
  J Mol Biol, 381, 1213-1223.
PDB code: 3coo
  19238248 L.Ayadi (2008).
Molecular modelling of the TSR domain of R-spondin 4.
  Bioinformation, 3, 119-123.  
17997122 M.E.Patarroyo, G.Cifuentes, and R.Rodríguez (2008).
Structural characterisation of sporozoite components for a multistage, multi-epitope, anti-malarial vaccine.
  Int J Biochem Cell Biol, 40, 543-557.  
19020352 M.Nagae, K.Nishikawa, N.Yasui, M.Yamasaki, T.Nogi, and J.Takagi (2008).
Structure of the F-spondin reeler domain reveals a unique beta-sandwich fold with a deformable disulfide-bonded loop.
  Acta Crystallogr D Biol Crystallogr, 64, 1138-1145.
PDB codes: 2zot 2zou
  18512339 V.B.Carruthers, and F.M.Tomley (2008).
Microneme proteins in apicomplexans.
  Subcell Biochem, 47, 33-45.  
17032646 K.Kozma, J.J.Keusch, B.Hegemann, K.B.Luther, D.Klein, D.Hess, R.S.Haltiwanger, and J.Hofsteenge (2006).
Identification and characterization of abeta1,3-glucosyltransferase that synthesizes the Glc-beta1,3-Fuc disaccharide on thrombospondin type 1 repeats.
  J Biol Chem, 281, 36742-36751.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.