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PDBsum entry 1jb3
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protein links
Cell adhesion PDB id
1jb3

 

 

 

 

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Contents
Protein chain
127 a.a.
Waters ×184
PDB id:
1jb3
Name: Cell adhesion
Title: The laminin-binding domain of agrin is structurally related to n-timp- 1
Structure: Agrin. Chain: a. Fragment: laminin-binding domain. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.198     R-free:   0.243
Authors: J.Stetefeld
Key ref:
J.Stetefeld et al. (2001). The laminin-binding domain of agrin is structurally related to N-TIMP-1. Nat Struct Biol, 8, 705-709. PubMed id: 11473262 DOI: 10.1038/90422
Date:
01-Jun-01     Release date:   08-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31696  (AGRIN_CHICK) -  Agrin from Gallus gallus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2081 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/90422 Nat Struct Biol 8:705-709 (2001)
PubMed id: 11473262  
 
 
The laminin-binding domain of agrin is structurally related to N-TIMP-1.
J.Stetefeld, M.Jenny, T.Schulthess, R.Landwehr, B.Schumacher, S.Frank, M.A.Rüegg, J.Engel, R.A.Kammerer.
 
  ABSTRACT  
 
Agrin is the key organizer of postsynaptic differentiation at the neuromuscular junction. This organization activity requires the binding of agrin to the synaptic basal lamina. Binding is conferred by the N-terminal agrin (NtA) domain, which mediates a high-affinity interaction with the coiled coil domain of laminins. Here, we report the crystal structure of chicken NtA at 1.6 A resolution. The structure reveals that NtA harbors an oligosaccharide/oligonucleotide-binding fold with several possible sites for the interaction with different ligands. A high structural similarity of NtA with the protease inhibition domain in tissue inhibitor of metalloproteinases-1 (TIMP-1) supports the idea of additional functions of agrin besides synaptogenic activity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo view of the section of the final 2.7 Å resolution 2F[o] - F[c] electron density map (blue; 1 contour level) around the N-terminal segment of the NtA structure in complex (starting with Cys 2). The chloride ion (red sphere) is trapped between Arg 5 and Ser 108. The free model of NtA in green (starting with Glu 6) is superimposed. Other than the rigidification of their N-terminal tail regions, the free and complexed structures are identical (overall r.m.s. deviation of 0.32 Å). 		Figure 4.
Figure 4. Electrostatic surface representation of the complexed NtA domain. a, Front view of the structure. N- and C-termini are to the left as in Fig. 1a. b, Back view of the NtA domain domain related to the representation in (a) rotated by 120° around the vertical axis. The molecular surface is shown in white, and negatively and positively charged side chains are colored red and blue, respectively.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 705-709) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397941 J.Cao, C.Sun, H.Zhao, Z.Xiao, B.Chen, J.Gao, T.Zheng, W.Wu, S.Wu, J.Wang, and J.Dai (2011).
The use of laminin modified linear ordered collagen scaffolds loaded with laminin-binding ciliary neurotrophic factor for sciatic nerve regeneration in rats.
  Biomaterials, 32, 3939-3948.  
20080133 K.Brew, and H.Nagase (2010).
The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity.
  Biochim Biophys Acta, 1803, 55-71.  
20207734 M.Bekhouche, D.Kronenberg, S.Vadon-Le Goff, C.Bijakowski, N.H.Lim, B.Font, E.Kessler, A.Colige, H.Nagase, G.Murphy, D.J.Hulmes, and C.Moali (2010).
Role of the netrin-like domain of procollagen C-proteinase enhancer-1 in the control of metalloproteinase activity.
  J Biol Chem, 285, 15950-15959.  
19845005 A.A.McFarlane, and J.Stetefeld (2009).
An interdomain disulfide bridge links the NtA and first FS domain in agrin.
  Protein Sci, 18, 2421-2428.
PDB code: 3i70
19955338 K.J.Hamill, K.Kligys, S.B.Hopkinson, and J.C.Jones (2009).
Laminin deposition in the extracellular matrix: a complex picture emerges.
  J Cell Sci, 122, 4409-4417.  
19587785 W.Sun, C.Sun, H.Zhao, H.Lin, Q.Han, J.Wang, H.Ma, B.Chen, Z.Xiao, and J.Dai (2009).
Improvement of sciatic nerve regeneration using laminin-binding human NGF-beta.
  PLoS One, 4, e6180.  
18956887 O.A.Ozhogina, A.Grishaev, E.L.Bominaar, L.Patthy, M.Trexler, and M.Llinás (2008).
NMR solution structure of the neurotrypsin Kringle domain.
  Biochemistry, 47, 12290-12298.
PDB codes: 2k4r 2k51
18414739 R.A.Williamson, P.Panagiotidou, J.D.Mott, and M.J.Howard (2008).
Dynamic characterisation of the netrin-like domain of human type 1 procollagen C-proteinase enhancer and comparison to the N-terminal domain of tissue inhibitor of metalloproteinases (TIMP).
  Mol Biosyst, 4, 417-425.  
17649979 C.O.Sallum, R.A.Kammerer, and A.T.Alexandrescu (2007).
Thermodynamic and structural studies of carbohydrate binding by the agrin-G3 domain.
  Biochemistry, 46, 9541-9550.  
  17237343 K.J.Greenlee, Z.Werb, and F.Kheradmand (2007).
Matrix metalloproteinases in lung: multiple, multifarious, and multifaceted.
  Physiol Rev, 87, 69-98.  
17525979 M.VanSaun, B.C.Humburg, M.G.Arnett, M.Pence, and M.J.Werle (2007).
Activation of Matrix Metalloproteinase-3 is altered at the frog neuromuscular junction following changes in synaptic activity.
  Dev Neurobiol, 67, 1488-1497.  
17126587 S.T.Ngo, P.G.Noakes, and W.D.Phillips (2007).
Neural agrin: a synaptic stabiliser.
  Int J Biochem Cell Biol, 39, 863-867.  
15598652 J.Bramham, C.T.Thai, D.C.Soares, D.Uhrín, R.T.Ogata, and P.N.Barlow (2005).
Functional insights from the structure of the multifunctional C345C domain of C5 of complement.
  J Biol Chem, 280, 10636-10645.
PDB code: 1xwe
12670942 E.Liepinsh, L.Banyai, G.Pintacuda, M.Trexler, L.Patthy, and G.Otting (2003).
NMR structure of the netrin-like domain (NTR) of human type I procollagen C-proteinase enhancer defines structural consensus of NTR domains and assesses potential proteinase inhibitory activity and ligand binding.
  J Biol Chem, 278, 25982-25989.
PDB code: 1uap
12554653 J.B.Mascarenhas, M.A.Rüegg, U.Winzen, W.Halfter, J.Engel, and J.Stetefeld (2003).
Mapping of the laminin-binding site of the N-terminal agrin domain (NtA).
  EMBO J, 22, 529-536.  
14627742 J.M.Aramini, Y.J.Huang, J.R.Cort, S.Goldsmith-Fischman, R.Xiao, L.Y.Shih, C.K.Ho, J.Liu, B.Rost, B.Honig, M.A.Kennedy, T.B.Acton, and G.T.Montelione (2003).
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
  Protein Sci, 12, 2823-2830.
PDB code: 1ny4
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.

 

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