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PDBsum entry 1b08
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protein metals Protein-protein interface(s) links
Sugar binding protein PDB id
1b08

 

 

 

 

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Contents
Protein chain
152 a.a. *
Metals
_CA ×9
Waters ×192
* Residue conservation analysis
PDB id:
1b08
Name: Sugar binding protein
Title: Lung surfactant protein d (sp-d) (fragment)
Structure: Protein (lung surfactant protein d). Chain: a, b, c. Fragment: trimeric fragment consisting of lectin domains and alpha- helical coiled-coil. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: lung. Tissue: pulmonary surfactant. Cellular_location: extra-cellular. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Biol. unit: Trimer (from PQS)
Resolution:
2.30Å     R-factor:   0.209     R-free:   0.271
Authors: K.Hakansson,N.K.Lim,H.-J.Hoppe,K.B.M.Reid
Key ref:
K.Håkansson et al. (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. PubMed id: 10368295 DOI: 10.1016/S0969-2126(99)80036-7
Date:
18-Nov-98     Release date:   01-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P35247  (SFTPD_HUMAN) -  Pulmonary surfactant-associated protein D from Homo sapiens
Seq:
Struc: 		375 a.a.
152 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(99)80036-7 Structure 7:255-264 (1999)
PubMed id: 10368295  
 
 
Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D.
K.Håkansson, N.K.Lim, H.J.Hoppe, K.B.Reid.
 
  ABSTRACT  
 
BACKGROUND: Human lung surfactant protein D (hSP-D) belongs to the collectin family of C-type lectins and participates in the innate immune surveillance against microorganisms in the lung through recognition of carbohydrate ligands present on the surface of pathogens. The involvement of this protein in innate immunity and the allergic response make it the subject of much interest. RESULTS: We have determined the crystal structure of a trimeric fragment of hSP-D at 2.3 A resolution. The structure comprises an alpha-helical coiled-coil and three carbohydrate-recognition domains (CRDs). An interesting deviation from symmetry was found in the projection of a single tyrosine sidechain into the centre of the coiled-coil; the asymmetry of this residue influences the orientation of one of the adjacent CRDs. The cleft between the three CRDs presents a large positively charged surface. CONCLUSIONS: The fold of the CRD of hSP-D is similar to that of the mannan-binding protein (MBP), but its orientation relative to the alpha-helical coiled-coil region differs somewhat to that seen in the MBP structure. The novel central packing of the tyrosine sidechain within the coiled-coil and the resulting asymmetric orientation of the CRDs has unexpected functional implications. The positively charged surface might facilitate binding to negatively charged structures, such as lipopolysaccharides.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The mainchain fold of hSP-D with consensus motifs highlighted: DGGS is in red and RACGEKR is in blue. Calcium ions are depicted as green spheres. (The figure was produced using the program RIBBONS [39].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 255-264) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.
  Cell Mol Immunol, 8, 265-275.  
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.  
20004639 R.Mendelsohn, G.Mao, and C.R.Flach (2010).
Infrared reflection-absorption spectroscopy: principles and applications to lipid-protein interaction in Langmuir films.
  Biochim Biophys Acta, 1798, 788-800.  
19177340 L.Knudsen, K.Wucherpfennig, R.M.Mackay, P.Townsend, C.Mühlfeld, J.Richter, S.Hawgood, K.Reid, H.Clark, and M.Ochs (2009).
A recombinant fragment of human surfactant protein D lacking the short collagen-like stalk fails to correct morphological alterations in lungs of SP-D deficient mice.
  Anat Rec (Hoboken), 292, 183-189.  
19405544 N.M.Plourde, S.Kortagere, W.Welsh, and P.V.Moghe (2009).
Structure-activity relations of nanolipoblockers with the atherogenic domain of human macrophage scavenger receptor A.
  Biomacromolecules, 10, 1381-1391.  
19631658 S.P.Boudko, T.Sasaki, J.Engel, T.F.Lerch, J.Nix, M.S.Chapman, and H.P.Bächinger (2009).
Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.
  J Mol Biol, 392, 787-802.
PDB codes: 3hon 3hsh
19684355 T.K.Carlson, J.B.Torrelles, K.Smith, T.Horlacher, R.Castelli, P.H.Seeberger, E.C.Crouch, and L.S.Schlesinger (2009).
Critical role of amino acid position 343 of surfactant protein-D in the selective binding of glycolipids from Mycobacterium tuberculosis.
  Glycobiology, 19, 1473-1484.  
16522803 D.H.Shin, J.S.Kim, H.Yokota, R.Kim, and S.H.Kim (2006).
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.
  Protein Sci, 15, 921-928.
PDB code: 2ba2
16636058 E.Crouch, B.McDonald, K.Smith, T.Cafarella, B.Seaton, and J.Head (2006).
Contributions of phenylalanine 335 to ligand recognition by human surfactant protein D: ring interactions with SP-D ligands.
  J Biol Chem, 281, 18008-18014.
PDB codes: 2ggu 2ggx
16423264 H.Chiba, S.Piboonpocanun, H.Mitsuzawa, K.Kuronuma, R.C.Murphy, and D.R.Voelker (2006).
Pulmonary surfactant proteins and lipids as modulators of inflammation and innate immunity.
  Respirology, 11, S2-S6.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15946251 D.Voulgaraki, R.Mitnacht-Kraus, M.Letarte, M.Foster-Cuevas, M.H.Brown, and A.N.Barclay (2005).
Multivalent recombinant proteins for probing functions of leucocyte surface proteins such as the CD200 receptor.
  Immunology, 115, 337-346.  
15711012 E.Crouch, Y.Tu, D.Briner, B.McDonald, K.Smith, U.Holmskov, and K.Hartshorn (2005).
Ligand specificity of human surfactant protein D: expression of a mutant trimeric collectin that shows enhanced interactions with influenza A virus.
  J Biol Chem, 280, 17046-17056.  
15509576 H.Feinberg, Y.Guo, D.A.Mitchell, K.Drickamer, and W.I.Weis (2005).
Extended neck regions stabilize tetramers of the receptors DC-SIGN and DC-SIGNR.
  J Biol Chem, 280, 1327-1335.
PDB code: 1xar
16150695 K.Okumura, A.Ohno, M.Nishida, K.Hayashi, K.Ikeda, and S.Inoue (2005).
Mapping the region of the alpha-type phospholipase A2 inhibitor responsible for its inhibitory activity.
  J Biol Chem, 280, 37651-37659.  
15319425 H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, and T.Hatakeyama (2004).
Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis.
  J Biol Chem, 279, 45219-45225.
PDB codes: 1wmy 1wmz
15030473 J.K.van de Wetering, L.M.van Golde, and J.J.Batenburg (2004).
Collectins: players of the innate immune system.
  Eur J Biochem, 271, 1229-1249.  
15145932 N.Palaniyar, J.Nadesalingam, H.Clark, M.J.Shih, A.W.Dodds, and K.B.Reid (2004).
Nucleic acid is a novel ligand for innate, immune pattern recognition collectins surfactant proteins A and D and mannose-binding lectin.
  J Biol Chem, 279, 32728-32736.  
15078883 T.O.Hirche, E.C.Crouch, M.Espinola, T.J.Brokelman, R.P.Mecham, N.DeSilva, J.Cooley, E.Remold-O'Donnell, and A.Belaaouaj (2004).
Neutrophil serine proteinases inactivate surfactant protein D by cleaving within a conserved subregion of the carbohydrate recognition domain.
  J Biol Chem, 279, 27688-27698.  
14660572 T.Ohashi, and H.P.Erickson (2004).
The disulfide bonding pattern in ficolin multimers.
  J Biol Chem, 279, 6534-6539.  
12920133 A.McAlinden, T.A.Smith, L.J.Sandell, D.Ficheux, D.A.Parry, and D.J.Hulmes (2003).
Alpha-helical coiled-coil oligomerization domains are almost ubiquitous in the collagen superfamily.
  J Biol Chem, 278, 42200-42207.  
12857753 F.X.McCormack, R.Gibbons, S.R.Ward, A.Kuzmenko, H.Wu, and G.S.Deepe (2003).
Macrophage-independent fungicidal action of the pulmonary collectins.
  J Biol Chem, 278, 36250-36256.  
  12750409 H.Wu, A.Kuzmenko, S.Wan, L.Schaffer, A.Weiss, J.H.Fisher, K.S.Kim, and F.X.McCormack (2003).
Surfactant proteins A and D inhibit the growth of Gram-negative bacteria by increasing membrane permeability.
  J Clin Invest, 111, 1589-1602.  
12913002 J.F.Head, T.R.Mealy, F.X.McCormack, and B.A.Seaton (2003).
Crystal structure of trimeric carbohydrate recognition and neck domains of surfactant protein A.
  J Biol Chem, 278, 43254-43260.
PDB codes: 1r13 1r14
12730206 J.Nadesalingam, A.L.Bernal, A.W.Dodds, A.C.Willis, D.J.Mahoney, A.J.Day, K.B.Reid, and N.Palaniyar (2003).
Identification and characterization of a novel interaction between pulmonary surfactant protein D and decorin.
  J Biol Chem, 278, 25678-25687.  
12524383 U.Holmskov, S.Thiel, and J.C.Jensenius (2003).
Collections and ficolins: humoral lectins of the innate immune defense.
  Annu Rev Immunol, 21, 547-578.  
12194968 A.McAlinden, E.C.Crouch, J.G.Bann, P.Zhang, and L.J.Sandell (2002).
Trimerization of the amino propeptide of type IIA procollagen using a 14-amino acid sequence derived from the coiled-coil neck domain of surfactant protein D.
  J Biol Chem, 277, 41274-41281.  
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.  
11181966 E.Crouch, and J.R.Wright (2001).
Surfactant proteins a and d and pulmonary host defense.
  Annu Rev Physiol, 63, 521-554.  
11592086 L.E.Haswell, M.J.Glennie, and A.Al-Shamkhani (2001).
Analysis of the oligomeric requirement for signaling by CD40 using soluble multimeric forms of its ligand, CD154.
  Eur J Immunol, 31, 3094-3100.  
11181965 S.Hawgood, and F.R.Poulain (2001).
The pulmonary collectins and surfactant metabolism.
  Annu Rev Physiol, 63, 495-519.  
  11045608 K.Håkansson, and K.B.Reid (2000).
Collectin structure: a review.
  Protein Sci, 9, 1607-1617.  
10828943 N.Palaniyar, F.X.McCormack, F.Possmayer, and G.Harauz (2000).
Three-dimensional structure of rat surfactant protein A trimers in association with phospholipid monolayers.
  Biochemistry, 39, 6310-6316.
PDB codes: 1du8 1gie
10508765 K.Drickamer (1999).
C-type lectin-like domains.
  Curr Opin Struct Biol, 9, 585-590.  
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.

 

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