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PDBsum entry 1egg

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protein metals Protein-protein interface(s) links
Sugar binding protein PDB id
1egg
Jmol
Contents
Protein chains
132 a.a. *
144 a.a. *
Metals
_CA ×3
Waters ×145
* Residue conservation analysis
PDB id:
1egg
Name: Sugar binding protein
Title: Structure of a c-type carbohydrate-recognition domain (crd- 4) from the macrophage mannose receptor
Structure: Macrophage mannose receptor. Chain: a, b. Fragment: carbohydrate-recognition domain 4. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.216     R-free:   0.278
Authors: H.Feinberg,S.Park-Snyder,A.R.Kolatkar,C.T.Heise,M.E.Taylor, W.I.Weis
Key ref:
H.Feinberg et al. (2000). Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor. J Biol Chem, 275, 21539-21548. PubMed id: 10779515 DOI: 10.1074/jbc.M002366200
Date:
15-Feb-00     Release date:   30-Aug-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22897  (MRC1_HUMAN) -  Macrophage mannose receptor 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1456 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P22897  (MRC1_HUMAN) -  Macrophage mannose receptor 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1456 a.a.
144 a.a.*
Key:    PfamA 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: 10.1074/jbc.M002366200 J Biol Chem 275:21539-21548 (2000)
PubMed id: 10779515  
 
 
Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor.
H.Feinberg, S.Park-Snyder, A.R.Kolatkar, C.T.Heise, M.E.Taylor, W.I.Weis.
 
  ABSTRACT  
 
The mannose receptor of macrophages and liver endothelium mediates clearance of pathogenic organisms and potentially harmful glycoconjugates. The extracellular portion of the receptor includes eight C-type carbohydrate recognition domains (CRDs), of which one, CRD-4, shows detectable binding to monosaccharide ligands. We have determined the crystal structure of CRD-4. Although the basic C-type lectin fold is preserved, a loop extends away from the core of the domain to form a domain-swapped dimer in the crystal. Of the two Ca(2+) sites, only the principal site known to mediate carbohydrate binding in other C-type lectins is occupied. This site is altered in a way that makes sugar binding impossible in the mode observed in other C-type lectins. The structure is likely to represent an endosomal form of the domain formed when Ca(2+) is lost from the auxiliary calcium site. The structure suggests a mechanism for endosomal ligand release in which the auxiliary calcium site serves as a pH sensor. Acid pH-induced removal of this Ca(2+) results in conformational rearrangements of the receptor, rendering it unable to bind carbohydrate ligands.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Flexibility of the extended loop region. The CRD cores of the two independent copies of mannose receptor CRD-4 ( brown, copy A; blue, copy B) have been superimposed along with the cores of the two subunits of the IX/X-BP (yellow and cyan).
Figure 5.
Fig. 5. Comparison of Ca^2+ binding in the principal site between mannose receptor CRD-4 (gray bonds), MBP-A (brown bonds), and E-selectin (yellow bonds). Red, blue, and green spheres represent oxygen, nitrogen, and calcium, respectively. Ca^2+ coordination bonds are shown as dashed lines and hydrogen bonds are shown as thin solid lines. In CRD-4, residues 725, 727, and 728 come from one protomer of the dimer, and 747 and 748 come from the other protomer. In A, and B, the residue numbers are from the mannose receptor, with the equivalent MBP-A (A) or E-selectin (B) residue numbers shown in parentheses. In C, MBP-A numbers are shown with equivalent residue numbers of E-selectin shown in parentheses.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 21539-21548) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20617143 Y.Ikehara, M.Yamanaka, and T.Yamaguchi (2010).
Recent advancements in cytotoxic T lymphocyte generation methods using carbohydrate-coated liposomes.
  J Biomed Biotechnol, 2010, 242539.  
19224860 J.Lai, O.K.Bernhard, S.G.Turville, A.N.Harman, J.Wilkinson, and A.L.Cunningham (2009).
Oligomerization of the macrophage mannose receptor enhances gp120-mediated binding of HIV-1.
  J Biol Chem, 284, 11027-11038.  
18509109 A.Bugarcic, K.Hitchens, A.G.Beckhouse, C.A.Wells, R.B.Ashman, and H.Blanchard (2008).
Human and mouse macrophage-inducible C-type lectin (Mincle) bind Candida albicans.
  Glycobiology, 18, 679-685.  
17163964 M.Butler, A.S.Morel, W.J.Jordan, E.Eren, S.Hue, R.E.Shrimpton, and M.A.Ritter (2007).
Altered expression and endocytic function of CD205 in human dendritic cells, and detection of a CD205-DCL-1 fusion protein upon dendritic cell maturation.
  Immunology, 120, 362-371.  
17193596 S.Boutry, S.Laurent, L.V.Elst, and R.N.Muller (2006).
Specific E-selectin targeting with a superparamagnetic MRI contrast agent.
  Contrast Media Mol Imaging, 1, 15-22.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15576563 P.Paaventhan, C.Kong, J.S.Joseph, M.C.Chung, and P.R.Kolatkar (2005).
Structure of rhodocetin reveals noncovalently bound heterodimer interface.
  Protein Sci, 14, 169-175.
PDB code: 1sb2
16170324 S.A.McMahon, J.L.Miller, J.A.Lawton, D.E.Kerkow, A.Hodes, M.A.Marti-Renom, S.Doulatov, E.Narayanan, A.Sali, J.F.Miller, and P.Ghosh (2005).
The C-type lectin fold as an evolutionary solution for massive sequence variation.
  Nat Struct Mol Biol, 12, 886-892.
PDB codes: 1yu0 1yu1 1yu2 1yu3 1yu4
12866057 A.N.Zelensky, and J.E.Gready (2003).
Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD).
  Proteins, 52, 466-477.  
12856000 A.Rivera-Calzada, D.Robertson, J.R.MacFadyen, J.Boskovic, C.M.Isacke, and O.Llorca (2003).
Three-dimensional interplay among the ligand-binding domains of the urokinase-plasminogen-activator-receptor-associated protein, Endo180.
  EMBO Rep, 4, 807-812.  
11866098 T.Hatakeyama, N.Matsuo, K.Shiba, S.Nishinohara, N.Yamasaki, H.Sugawara, and H.Aoyagi (2002).
Amino acid sequence and carbohydrate-binding analysis of the N-acetyl-D-galactosamine-specific C-type lectin, CEL-I, from the Holothuroidea, Cucumaria echinata.
  Biosci Biotechnol Biochem, 66, 157-163.  
11785767 H.Kogelberg, and T.Feizi (2001).
New structural insights into lectin-type proteins of the immune system.
  Curr Opin Struct Biol, 11, 635-643.  
11471734 I.Sallay, S.Tojo, K.Nomiyama, Y.Kouzuma, M.Kimura, and N.Yamasaki (2001).
Calcium ions stabilize a protein structure of hemolytic lectin CEL-III from marine invertebrate Cucumaria echinata.
  Biosci Biotechnol Biochem, 65, 1347-1352.  
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.