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PDBsum entry 1tn3

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protein ligands metals links
Lectin PDB id
1tn3
Jmol
Contents
Protein chain
137 a.a. *
Ligands
SO4
EOH
Metals
_CA ×2
Waters ×63
* Residue conservation analysis
PDB id:
1tn3
Name: Lectin
Title: ThE C-type lectin carbohydrate recognition domain of human tetranectin
Structure: Tetranectin. Chain: a. Fragment: residues 45 - 181. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.218     R-free:   0.260
Authors: J.S.Kastrup,B.B.Nielsen,H.Rasmussen,T.L.Holtet, J.H.Graversen,M.Etzerodt,H.C.Thoegersen,I.K.Larsen
Key ref:
J.S.Kastrup et al. (1998). Structure of the C-type lectin carbohydrate recognition domain of human tetranectin. Acta Crystallogr D Biol Crystallogr, 54, 757-766. PubMed id: 9757090 DOI: 10.1107/S0907444997016806
Date:
06-Nov-97     Release date:   06-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05452  (TETN_HUMAN) -  Tetranectin
Seq:
Struc:
202 a.a.
137 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1107/S0907444997016806 Acta Crystallogr D Biol Crystallogr 54:757-766 (1998)
PubMed id: 9757090  
 
 
Structure of the C-type lectin carbohydrate recognition domain of human tetranectin.
J.S.Kastrup, B.B.Nielsen, H.Rasmussen, T.L.Holtet, J.H.Graversen, M.Etzerodt, H.C.Thøgersen, I.K.Larsen.
 
  ABSTRACT  
 
Tetranectin (TN) is a C-type lectin involved in fibrinolysis, being the only endogenous ligand known to bind specifically to the kringle 4 domain of plasminogen. TN was originally isolated from plasma, but shows a wide tissue distribution. Furthermore, TN has been found in the extracellular matrix of certain human carcinomas, whereas none or little is present in the corresponding normal tissue. The crystal structure of full-length trimeric TN (2.8 A resolution) has recently been published [Nielsen et al. (1997). FEBS Lett. 412, 388-396]. The crystal structure of the carbohydrate recognition domain (CRD) of human TN (TN3) has been determined separately at 2.0 A resolution in order to obtain detailed information on the two calcium binding sites. This information is essential for the elucidation of the specificity of TN towards oligosaccharides. TN3 crystallizes as a dimer, whereas it appears as a monomer in solution. The overall fold of TN3 is similar to other known CRDs. Each monomer is built of two distinct regions, one region consisting of six beta-strands and two alpha-helices, and the other region is composed of four loops harboring two calcium ions. The calcium ion at site 1 forms an eightfold coordinated complex and has Asp116, Glu120, Gly147, Glu150, Asn151, and one water molecule as ligands. The calcium ion at site 2, which is believed to be involved in recognition and binding of oligosaccharides, is sevenfold coordinated with ligands Gln143, Asp145, Glu150, Asp165, and two water molecules. One sulfate ion has been located at the surface of TN3, forming contacts to Glu120, Lys148, Asn106 of a symmetry-related molecule, and to an ethanol molecule.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. A tube representation of TN3 and the CRD of rMBP from serum (r.m.s. of 0.96 A for 108 Ca atoms). The four loops (L1-L4) of TN3 are shown in yellow and of rMBP in magenta. The remaining residues of the two structures are uncolored. The calcium ions are shown as yellow and magenta spheres, respectively. The position of the calcium ions at site 1 is almost identical in the two structures. The figure was generated using MOLSCRIPT (Kraulis, 1991).
Figure 7.
Fig. 7. (a) Surface electrostatic potential of TN3. Potentials were calculated and rendered by the use of the program GRASP (Nichols et al., 1991). Negative potentials are colored in red, positive potentials in blue. The calcium binding sites 1 and 2 are indicated as well as the sulfate binding site. (b) As in (a), but rotated by 180 around the vertical axis. (c) The sulfate binding site of TN. The electron densities (2F o -Fc) for the sulfate ion (SO4) and the ethanol molecule (Eth) are shown, contoured at a level of 1.0a. Hydrogen bonds are depicted as dotted lines. The figure was generated using the program O (Jones et al., 1991).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1998, 54, 757-766) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18687680 J.P.Gourdine, G.Cioci, L.Miguet, C.Unverzagt, D.V.Silva, A.Varrot, C.Gautier, E.J.Smith-Ravin, and A.Imberty (2008).
High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry.
  J Biol Chem, 283, 30112-30120.
PDB codes: 2vuv 2vuz
17055245 D.S.Gill, and N.K.Damle (2006).
Biopharmaceutical drug discovery using novel protein scaffolds.
  Curr Opin Biotechnol, 17, 653-658.  
15585533 E.Zhao, H.L.Liu, C.H.Tsai, H.K.Tsai, C.H.Chan, and C.Y.Kao (2005).
Cysteine separations profiles on protein sequences infer disulfide connectivity.
  Bioinformatics, 21, 1415-1420.  
16054718 T.Hey, E.Fiedler, R.Rudolph, and M.Fiedler (2005).
Artificial, non-antibody binding proteins for pharmaceutical and industrial applications.
  Trends Biotechnol, 23, 514-522.  
15296743 A.Lundell, A.I.Olin, M.Mörgelin, S.al-Karadaghi, A.Aspberg, and D.T.Logan (2004).
Structural basis for interactions between tenascins and lectican C-type lectin domains: evidence for a crosslinking role for tenascins.
  Structure, 12, 1495-1506.
PDB code: 1tdq
14717962 J.H.Geiger, and S.E.Cnudde (2004).
What the structure of angiostatin may tell us about its mechanism of action.
  J Thromb Haemost, 2, 23-34.  
12945048 S.Ebner, N.Sharon, and N.Ben-Tal (2003).
Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily.
  Proteins, 53, 44-55.  
11861620 K.Natarajan, N.Dimasi, J.Wang, R.A.Mariuzza, and D.H.Margulies (2002).
Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
  Annu Rev Immunol, 20, 853-885.  
11432819 C.Grégoire, S.Marco, J.Thimonier, L.Duplan, E.Laurine, J.P.Chauvin, B.Michel, V.Peyrot, and J.M.Verdier (2001).
Three-dimensional structure of the lithostathine protofibril, a protein involved in Alzheimer's disease.
  EMBO J, 20, 3313-3321.  
11746888 R.Zeng, Q.Xu, X.X.Shao, K.Y.Wang, and Q.C.Xia (2001).
Determination of the disulfide bond pattern of a novel C-type lectin from snake venom by mass spectrometry.
  Rapid Commun Mass Spectrom, 15, 2213-2220.  
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10607664 M.Vijayan, and N.Chandra (1999).
Lectins.
  Curr Opin Struct Biol, 9, 707-714.  
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 codes are shown on the right.