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PDBsum entry 1msb
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protein metals Protein-protein interface(s) links
Hepatic lectin PDB id
1msb

 

 

 

 

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Contents
Protein chains
115 a.a. *
Metals
_HO ×4
Waters ×57
* Residue conservation analysis
PDB id:
1msb
Name: Hepatic lectin
Title: Structure of the calcium-dependent lectin domain from a rat mannose- binding protein determined by mad phasing
Structure: Mannose-binding protein-a. Chain: a, b. Engineered: yes
Source: Rattus rattus. Black rat. Organism_taxid: 10117
Resolution:
2.30Å     R-factor:   0.176    
Authors: W.I.Weis,K.Drickamer,W.A.Hendrickson
Key ref: W.I.Weis et al. (1991). Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science, 254, 1608-1615. PubMed id: 1721241 DOI: 10.1126/science.1721241
Date:
23-Sep-91     Release date:   15-Jan-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19999  (MBL1_RAT) -  Mannose-binding protein A from Rattus norvegicus
Seq:
Struc: 		238 a.a.
115 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1126/science.1721241 Science 254:1608-1615 (1991)
PubMed id: 1721241  
 
 
Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing.
W.I.Weis, R.Kahn, R.Fourme, K.Drickamer, W.A.Hendrickson.
 
  ABSTRACT  
 
Calcium-dependent (C-type) animal lectins participate in many cell surface recognition events mediated by protein-carbohydrate interactions. The C-type lectin family includes cell adhesion molecules, endocytic receptors, and extracellular matrix proteins. Mammalian mannose-binding proteins are C-type lectins that function in antibody-independent host defense against pathogens. The crystal structure of the carbohydrate-recognition domain of a rat mannose-binding protein, determined as the holmium-substituted complex by multiwavelength anomalous dispersion (MAD) phasing, reveals an unusual fold consisting of two distinct regions, one of which contains extensive nonregular secondary structure stabilized by two holmium ions. The structure explains the conservation of 32 residues in all C-type carbohydrate-recognition domains, suggesting that the fold seen here is common to these domains. The strong anomalous scattering observed at the Ho LIII edge demonstrates that traditional heavy atom complexes will be generally amenable to the MAD phasing method.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21269602 J.Brasch, O.J.Harrison, G.Ahlsen, S.M.Carnally, R.M.Henderson, B.Honig, and L.Shapiro (2011).
Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.
  J Mol Biol, 408, 57-73.
PDB code: 3ppe
21383675 M.Wang, Y.Chen, Y.Zhang, L.Zhang, X.Lu, and Z.Chen (2011).
Mannan-binding lectin directly interacts with Toll-like receptor 4 and suppresses lipopolysaccharide-induced inflammatory cytokine secretion from THP-1 cells.
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21194488 M.Wang, Y.Zhang, Y.Chen, L.Zhang, X.Lu, and Z.Chen (2011).
Mannan-binding lectin regulates dendritic cell maturation and cytokine production induced by lipopolysaccharide.
  BMC Immunol, 12, 1.  
21169697 R.Talon, R.Kahn, M.A.Durá, O.Maury, F.M.Vellieux, B.Franzetti, and E.Girard (2011).
Using lanthanoid complexes to phase large macromolecular assemblies.
  J Synchrotron Radiat, 18, 74-78.  
20193029 A.M.Kerrigan, and G.D.Brown (2010).
Syk-coupled C-type lectin receptors that mediate cellular activation via single tyrosine based activation motifs.
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20606256 G.Pompidor, O.Maury, J.Vicat, and R.Kahn (2010).
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PDB codes: 2pe7 2pes 3lgr
20032175 H.P.Su, K.Singh, A.G.Gittis, and D.N.Garboczi (2010).
The structure of the poxvirus A33 protein reveals a dimer of unique C-type lectin-like domains.
  J Virol, 84, 2502-2510.
PDB code: 3k7b
20544345 L.M.Flornes, Ã.˜.Nylenna, P.C.Saether, M.R.Daws, E.Dissen, and S.Fossum (2010).
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19380589 A.K.Schnitger, H.Yassine, F.C.Kafatos, and M.A.Osta (2009).
Two C-type lectins cooperate to defend Anopheles gambiae against Gram-negative bacteria.
  J Biol Chem, 284, 17616-17624.  
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  Proc Natl Acad Sci U S A, 106, 11524-11529.  
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.
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High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry.
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PDB codes: 2vuv 2vuz
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PDB codes: 3c8j 3c8k 3cad
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Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.
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PDB codes: 2ox8 2ox9
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PDB codes: 2h2r 2h2t
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PDB code: 2b6b
16373473 J.H.Brown (2006).
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16948640 R.M.Dommett, N.Klein, and M.W.Turner (2006).
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15760448 A.Cambi, M.Koopman, and C.G.Figdor (2005).
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PDB code: 1gzt
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Conformation of a trimannoside bound to mannose-binding protein by nuclear magnetic resonance and molecular dynamics simulations.
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Identification of human mannose binding lectin (MBL) recognition sites for novel inhibitory antibodies.
  Hybrid Hybridomics, 21, 25-36.  
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Structural and functional characterization of a C-type lectin-like antifreeze protein from rainbow smelt (Osmerus mordax).
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Thiol-reactive lanthanide chelates for phasing protein X-ray diffraction data.
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Molecular cloning of mouse collectin liver 1.
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3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
12762005 D.E.Brodersen, A.P.Carter, W.M.Clemons, R.J.Morgan-Warren, F.V.Murphy, J.M.Ogle, M.J.Tarry, B.T.Wimberly, and V.Ramakrishnan (2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
  Cold Spring Harb Symp Quant Biol, 66, 17-32.  
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.  
11536172 I.Arce, P.Roda-Navarro, M.C.Montoya, P.Hernanz-Falcón, A.Puig-Kröger, and E.Fernández-Ruiz (2001).
Molecular and genomic characterization of human DLEC, a novel member of the C-type lectin receptor gene family preferentially expressed on monocyte-derived dendritic cells.
  Eur J Immunol, 31, 2733-2740.  
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.  
11181965 S.Hawgood, and F.R.Poulain (2001).
The pulmonary collectins and surfactant metabolism.
  Annu Rev Physiol, 63, 495-519.  
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
10771434 B.B.Nielsen, J.S.Kastrup, H.Rasmussen, J.H.Graversen, M.Etzerodt, H.C.Thøgersen, and I.K.Larsen (2000).
Crystallization and molecular-replacement solution of a truncated form of human recombinant tetranectin.
  Acta Crystallogr D Biol Crystallogr, 56, 637-639.  
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
11101293 K.Natarajan, M.W.Sawicki, D.H.Margulies, and R.A.Mariuzza (2000).
Crystal structure of human CD69: a C-type lectin-like activation marker of hematopoietic cells.
  Biochemistry, 39, 14779-14786.
PDB code: 1fm5
10903954 T.J.Boggon, and L.Shapiro (2000).
Screening for phasing atoms in protein crystallography.
  Structure, 8, R143-R149.  
11081633 W.S.Somers, J.Tang, G.D.Shaw, and R.T.Camphausen (2000).
Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1.
  Cell, 103, 467-479.
PDB codes: 1g1q 1g1r 1g1s 1g1t
10089396 G.Evans, and K.S.Wilson (1999).
A MAD experiment performed at the white line of the iridium LIII absorption edge in lysozyme.
  Acta Crystallogr D Biol Crystallogr, 55, 67-76.  
10023772 J.C.Boyington, A.N.Riaz, A.Patamawenu, J.E.Coligan, A.G.Brooks, and P.D.Sun (1999).
Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors.
  Immunity, 10, 75-82.
PDB code: 1b6e
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
10368295 K.Håkansson, N.K.Lim, H.J.Hoppe, and K.B.Reid (1999).
Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D.
  Structure, 7, 255-264.
PDB code: 1b08
10329779 M.A.Walsh, I.Dementieva, G.Evans, R.Sanishvili, and A.Joachimiak (1999).
Taking MAD to the extreme: ultrafast protein structure determination.
  Acta Crystallogr D Biol Crystallogr, 55, 1168-1173.
PDB code: 1srv
10089356 Z.Chen, E.Blanc, and M.S.Chapman (1999).
Real-space molecular-dynamics structure refinement.
  Acta Crystallogr D Biol Crystallogr, 55, 464-468.  
  9529088 A.F.Swanson, R.A.Ezekowitz, A.Lee, and C.C.Kuo (1998).
Human mannose-binding protein inhibits infection of HeLa cells by Chlamydia trachomatis.
  Infect Immun, 66, 1607-1612.  
9562557 D.E.Brodersen, M.Etzerodt, P.Madsen, J.E.Celis, H.C.Thøgersen, J.Nyborg, and M.Kjeldgaard (1998).
EF-hands at atomic resolution: the structure of human psoriasin (S100A7) solved by MAD phasing.
  Structure, 6, 477-489.
PDB code: 1psr
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Crystal structure of the angiogenesis inhibitor endostatin at 1.5 A resolution.
  EMBO J, 17, 1656-1664.
PDB code: 1koe
9761907 G.Zhou, J.Wang, E.Blanc, and M.S.Chapman (1998).
Determination of the relative precision of atoms in a macromolecular structure.
  Acta Crystallogr D Biol Crystallogr, 54, 391-399.  
9786953 M.L.Borowsky, and R.O.Hynes (1998).
Layilin, a novel talin-binding transmembrane protein homologous with C-type lectins, is localized in membrane ruffles.
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Genetic heterogeneity of mannose-binding proteins: the Jekyll and Hyde of innate immunity?
  Am J Hum Genet, 62, 6-9.  
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Cloning and sequencing of a cDNA encoding chicken mannan-binding lectin (MBL) and comparison with mammalian analogues.
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MAFA-L, an ITIM-containing receptor encoded by the human NK cell gene complex and expressed by basophils and NK cells.
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The C-type lectin superfamily in the immune system.
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9187649 H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, H.Atoda, and T.Morita (1997).
Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains.
  Nat Struct Biol, 4, 438-441.
PDB code: 1ixx
9108235 J.Johansson, and T.Curstedt (1997).
Molecular structures and interactions of pulmonary surfactant components.
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Aerolysin and pertussis toxin share a common receptor-binding domain.
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Tetranectin, a trimeric plasminogen-binding C-type lectin.
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9016719 V.C.Yee, K.P.Pratt, H.C.Côté, I.L.Trong, D.W.Chung, E.W.Davie, R.E.Stenkamp, and D.C.Teller (1997).
Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen.
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PDB codes: 1fib 1fic 1fid
9345619 W.I.Weis (1997).
Cell-surface carbohydrate recognition by animal and viral lectins.
  Curr Opin Struct Biol, 7, 624-630.  
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Solution structure of the link module: a hyaluronan-binding domain involved in extracellular matrix stability and cell migration.
  Cell, 86, 767-775.
PDB code: 1tsg
8913682 H.S.Pappa, A.E.Stewart, and N.Q.McDonald (1996).
Incorporating anomalous scattering centres into macromolecules.
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Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation.
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PDB code: 1lit
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Structure-based modeling of the ligand binding domain of the human cell surface receptor CD23 and comparison of two independently derived molecular models.
  Protein Sci, 5, 240-247.
PDB code: 1kje
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The collectins in innate immunity.
  Curr Opin Immunol, 8, 29-35.  
8924200 K.C.Chou (1996).
Knowledge-based model building of the tertiary structures for lectin domains of the selectin family.
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As MAD as can be.
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Principles of protein-protein interactions.
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Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin.
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PDB codes: 1aqz 1ar3
8749360 D.I.Stuart, and E.Y.Jones (1995).
Recognition at the cell surface: recent structural insights.
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8749859 D.Pignol, J.A.Bertrand, J.P.Bernard, J.M.Verdier, J.C.Dagorn, and J.C.Fontecilla-Camps (1995).
Crystallization and preliminary crystallographic study of human lithostathine.
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Galactosyl receptor in human testis and sperm is antigenically related to the minor C-type (Ca(2+)-dependent) lectin variant of human and rat liver.
  Mol Reprod Dev, 40, 460-466.  
  7540906 F.D.Sönnichsen, B.D.Sykes, and P.L.Davies (1995).
Comparative modeling of the three-dimensional structure of type II antifreeze protein.
  Protein Sci, 4, 460-471.  
8588938 J.R.Mertz, P.W.Banda, and A.L.Kierszenbaum (1995).
Rat sperm galactosyl receptor: purification and identification by polyclonal antibodies raised against multiple antigen peptides.
  Mol Reprod Dev, 41, 374-383.  
8574696 K.Drickamer (1995).
Increasing diversity of animal lectin structures.
  Curr Opin Struct Biol, 5, 612-616.  
7568140 M.D.Guthmann, M.Tal, and I.Pecht (1995).
A secretion inhibitory signal transduction molecule on mast cells is another C-type lectin.
  Proc Natl Acad Sci U S A, 92, 9397-9401.  
  7796798 N.Q.McDonald, N.Panayotatos, and W.A.Hendrickson (1995).
Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing.
  EMBO J, 14, 2689-2699.
PDB code: 1cnt
7480062 O.Ohara, J.Ishizaki, and H.Arita (1995).
Structure and function of phospholipase A2 receptor.
  Prog Lipid Res, 34, 117-138.  
  7591992 R.A.Dwek, A.C.Lellouch, and M.R.Wormald (1995).
Glycobiology: 'the function of sugar in the IgG molecule'.
  J Anat, 187, 279-292.  
8108426 D.I.Liao, G.Kapadia, H.Ahmed, G.R.Vasta, and O.Herzberg (1994).
Structure of S-lectin, a developmentally regulated vertebrate beta-galactoside-binding protein.
  Proc Natl Acad Sci U S A, 91, 1428-1432.
PDB code: 1slt
7712288 G.Wagner, and D.F.Wyss (1994).
Cell surface adhesion receptors.
  Curr Opin Struct Biol, 4, 841-851.  
7925387 H.Atoda, N.Yoshida, M.Ishikawa, and T.Morita (1994).
Binding properties of the coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis.
  Eur J Biochem, 224, 703-708.  
  7987210 H.J.Hoppe, and K.B.Reid (1994).
Collectins--soluble proteins containing collagenous regions and lectin domains--and their roles in innate immunity.
  Protein Sci, 3, 1143-1158.  
7704523 H.J.Hoppe, and K.B.Reid (1994).
Trimeric C-type lectin domains in host defence.
  Structure, 2, 1129-1133.  
8153870 K.B.Reid, and M.W.Turner (1994).
Mammalian lectins in activation and clearance mechanisms involving the complement system.
  Springer Semin Immunopathol, 15, 307-326.  
7544682 L.A.Lasky (1994).
A sweet success.
  Nat Struct Biol, 1, 139-141.  
7634099 P.E.Stein, A.Boodhoo, G.D.Armstrong, L.D.Heerze, S.A.Cockle, M.H.Klein, and R.J.Read (1994).
Structure of a pertussis toxin-sugar complex as a model for receptor binding.
  Nat Struct Biol, 1, 591-596.
PDB code: 1pto
8075982 P.E.Stein, A.Boodhoo, G.D.Armstrong, S.A.Cockle, M.H.Klein, and R.J.Read (1994).
The crystal structure of pertussis toxin.
  Structure, 2, 45-57.
PDB code: 1prt
8296164 P.Holt, U.Holmskov, S.Thiel, B.Teisner, P.Højrup, and J.C.Jensenius (1994).
Purification and characterization of mannan-binding protein from mouse serum.
  Scand J Immunol, 39, 202-208.  
7712290 P.M.Colman (1994).
Structure-based drug design.
  Curr Opin Struct Biol, 4, 868-874.  
7634089 S.Sheriff, C.Y.Chang, and R.A.Ezekowitz (1994).
Human mannose-binding protein carbohydrate recognition domain trimerizes through a triple alpha-helical coiled-coil.
  Nat Struct Biol, 1, 789-794.
PDB code: 1hup
7520818 W.I.Weis (1994).
Lectins on a roll: the structure of E-selectin.
  Structure, 2, 147-150.  
7704532 W.I.Weis, and K.Drickamer (1994).
Trimeric structure of a C-type mannose-binding protein.
  Structure, 2, 1227-1240.
PDB code: 1rtm
  8251933 A.W.Chan, E.G.Hutchinson, D.Harris, and J.M.Thornton (1993).
Identification, classification, and analysis of beta-bulges in proteins.
  Protein Sci, 2, 1574-1590.  
8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
7679675 D.V.Erbe, S.R.Watson, L.G.Presta, B.A.Wolitzky, C.Foxall, B.K.Brandley, and L.A.Lasky (1993).
P- and E-selectin use common sites for carbohydrate ligand recognition and cell adhesion.
  J Cell Biol, 120, 1227-1235.  
  7505680 J.Bajorath, R.Stenkamp, and A.Aruffo (1993).
Knowledge-based model building of proteins: concepts and examples.
  Protein Sci, 2, 1798-1810.
PDB code: 1kjd
  7689792 J.W.Fries, A.J.Williams, R.C.Atkins, W.Newman, M.F.Lipscomb, and T.Collins (1993).
Expression of VCAM-1 and E-selectin in an in vivo model of endothelial activation.
  Am J Pathol, 143, 725-737.  
8452675 K.Sastry, and R.A.Ezekowitz (1993).
Collectins: pattern recognition molecules involved in first line host defense.
  Curr Opin Immunol, 5, 59-66.  
8346557 N.Sharon (1993).
Lectin-carbohydrate complexes of plants and animals: an atomic view.
  Trends Biochem Sci, 18, 221-226.  
8509458 R.Horstkorte, M.Schachner, J.P.Magyar, T.Vorherr, and B.Schmitz (1993).
The fourth immunoglobulin-like domain of NCAM contains a carbohydrate recognition domain for oligomannosidic glycans implicated in association with L1 and neurite outgrowth.
  J Cell Biol, 121, 1409-1421.  
1382077 D.V.Erbe, B.A.Wolitzky, L.G.Presta, C.R.Norton, R.J.Ramos, D.K.Burns, J.M.Rumberger, B.N.Rao, C.Foxall, and B.K.Brandley (1992).
Identification of an E-selectin region critical for carbohydrate recognition and cell adhesion.
  J Cell Biol, 119, 215-227.  
1368439 J.A.Tainer, V.A.Roberts, and E.D.Getzoff (1992).
Protein metal-binding sites.
  Curr Opin Biotechnol, 3, 378-387.  
1460414 M.Matsushita, and T.Fujita (1992).
Activation of the classical complement pathway by mannose-binding protein in association with a novel C1s-like serine protease.
  J Exp Med, 176, 1497-1502.  
1303250 M.Super, S.D.Gillies, S.Foley, K.Sastry, J.E.Schweinle, V.J.Silverman, and R.A.Ezekowitz (1992).
Distinct and overlapping functions of allelic forms of human mannose binding protein.
  Nat Genet, 2, 50-55.  
15335991 R.A.Ezekowitz (1992).
Antigens coming to a sticky end.
  Curr Biol, 2, 147-149.  
1285423 R.D.Cummings, and D.F.Smith (1992).
The selectin family of carbohydrate-binding proteins: structure and importance of carbohydrate ligands for cell adhesion.
  Bioessays, 14, 849-856.  
  1304888 R.F.Doolittle (1992).
A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.
  Protein Sci, 1, 1563-1577.  
15335996 W.A.Hendrickson (1992).
Modes of transduction.
  Curr Biol, 2, 57-59.  
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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