PDBsum entry 1by2

Extracellular module

PDB id

1by2

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Contents

			Protein chain

					112 a.a. *

			Ligands

					NAG

			Waters ×57

* Residue conservation analysis

PDB id:

1by2

Links

Name:

Extracellular module

Title:

Structure of m2bp scavenger receptor cysteine-rich domain

Structure:

Mac-2 binding protein. Chain: a. Fragment: scavenger receptor cysteine-rich (srcr) domain. Synonym: tumor-associated antigen 90k. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: 293-ebna. Organ: kidney. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: 293-ebna.

Resolution:

2.00Å

R-factor:

0.186

R-free:

0.218

Authors:

E.Hohenester,T.Sasaki,R.Timpl

Key ref:

E.Hohenester et al. (1999). Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily. Nat Struct Biol, 6, 228-232. PubMed id: 10074941 DOI: 10.1038/6669

Date:

23-Oct-98

Release date:

18-May-99

PROCHECK

	Headers

	References

Protein chain

Q08380 (LG3BP_HUMAN) - Galectin-3-binding protein from Homo sapiens

Seq: Struc:

Seq: Struc:					585 a.a. 112 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1038/6669	Nat Struct Biol 6:228-232 (1999)
PubMed id: 10074941

Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily.
E.Hohenester, T.Sasaki, R.Timpl.

ABSTRACT

Scavenger receptor cysteine-rich (SRCR) domains are found widely in cell surface molecules and in some secreted proteins, where they are thought to mediate ligand binding. We have determined the crystal structure at 2.0 A resolution of the SRCR domain of Mac-2 binding protein (M2BP), a tumor-associated antigen and matrix protein. The structure reveals a curved six-stranded beta-sheet cradling an alpha-helix. Structure-based sequence alignment demonstrates that the M2BP SRCR domain is a valid template for the entire SRCR protein superfamily. This allows an interpretation of previous mutagenesis data on ligand binding to the lymphocyte receptor CD6.

Selected figure(s)



	Figure 1. Figure 1. Two orthogonal views^32 of the M2BP SRCR domain structure. -strands are in green and are labeled sequentially A−F; the -helix is in pink. Disulfide bridges are in yellow and the sequence numbers of cysteine residues are indicated.		Figure 4. Figure 4. Stereo view of the experimental electron density map after solvent flattening at 3.0 Å resolution. The map is contoured at the 1.0 level and the final refined model is superimposed on the map. Shown is the region around -strand B and the B−C hairpin. Made with BOBSCRIPT^33.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference Google scholar

PubMed id

Reference

20306300

Y.M.Kim, E.C.Kim, and Y.Kim (2011).
The human lysyl oxidase-like 2 protein functions as an amine oxidase toward collagen and elastin.

Mol Biol Rep, 38, 145-149.

20419315

A.Kuehn, N.Simon, and G.Pradel (2010).
Family members stick together: multi-protein complexes of malaria parasites.

Med Microbiol Immunol, 199, 209-226.

19935380

D.Malamud, and S.M.Wahl (2010).
The mouth: a gateway or a trap for HIV?

AIDS, 24, 5.

20016463

F.Bienaime, M.A.Dragon-Durey, C.H.Regnier, S.C.Nilsson, W.H.Kwan, J.Blouin, M.Jablonski, N.Renault, M.A.Rameix-Welti, C.Loirat, C.Sautés-Fridman, B.O.Villoutreix, A.M.Blom, and V.Fremeaux-Bacchi (2010).
Mutations in components of complement influence the outcome of Factor I-associated atypical hemolytic uremic syndrome.

Kidney Int, 77, 339-349.

19659436

M.J.Nielsen, H.J.Møller, and S.K.Moestrup (2010).
Hemoglobin and heme scavenger receptors.

Antioxid Redox Signal, 12, 261-273.

20162464

T.Li, D.Li, L.Cheng, H.Wu, Z.Gao, Z.Liu, W.Jiang, Y.H.Gao, F.Tian, L.Zhao, and S.Wang (2010).
Epithelial-mesenchymal transition induced by hepatitis C virus core protein in cholangiocarcinoma.

Ann Surg Oncol, 17, 1937-1944.

19120472

D.M.Bowdish, and S.Gordon (2009).
Conserved domains of the class A scavenger receptors: evolution and function.

Immunol Rev, 227, 19-31.

19065647

S.C.Nilsson, L.A.Trouw, N.Renault, M.A.Miteva, F.Genel, M.Zelazko, H.Marquart, K.Muller, A.G.Sjöholm, L.Truedsson, B.O.Villoutreix, and A.M.Blom (2009).
Genetic, molecular and functional analyses of complement factor I deficiency.

Eur J Immunol, 39, 310-323.

19015874

S.Sebban, B.Davidson, and R.Reich (2009).
Lysyl oxidase-like 4 is alternatively spliced in an anatomic site-specific manner in tumors involving the serosal cavities.

Virchows Arch, 454, 71-79.

18707547

R.Alonso, V.Huerta, J.de Leon, P.Piedra, Y.Puchades, O.Guirola, G.Chinea, and E.Montero (2008).
Towards the definition of a chimpanzee and human conserved CD6 domain 1 epitope recognized by T1 monoclonal antibody.

Hybridoma (Larchmt), 27, 291-301.

18020944

A.J.Ligtenberg, E.C.Veerman, A.V.Nieuw Amerongen, and J.Mollenhauer (2007).
Salivary agglutinin/glycoprotein-340/DMBT1: a single molecule with variable composition and with different functions in infection, inflammation and cancer.

Biol Chem, 388, 1275-1289.

17322294

B.Rodamilans, I.G.Muñoz, E.Bragado-Nilsson, M.R.Sarrias, O.Padilla, F.J.Blanco, F.Lozano, and G.Montoya (2007).
Crystal structure of the third extracellular domain of CD5 reveals the fold of a group B scavenger cysteine-rich receptor domain.

J Biol Chem, 282, 12669-12677.

PDB codes:

2ja4 2ott

17905828

C.A.Martin, E.Longman, C.Wooding, S.J.Hoosdally, S.Ali, T.J.Aitman, D.A.Gutmann, P.S.Freemont, B.Byrne, and K.J.Linton (2007).
Cd36, a class B scavenger receptor, functions as a monomer to bind acetylated and oxidized low-density lipoproteins.

Protein Sci, 16, 2531-2541.

17405873

J.R.Ojala, T.Pikkarainen, A.Tuuttila, T.Sandalova, and K.Tryggvason (2007).
Crystal structure of the cysteine-rich domain of scavenger receptor MARCO reveals the presence of a basic and an acidic cluster that both contribute to ligand recognition.

J Biol Chem, 282, 16654-16666.

PDB codes:

2oy3 2oya

17089378

R.E.Saunders, C.Abarrategui-Garrido, V.Frémeaux-Bacchi, E.Goicoechea de Jorge, T.H.Goodship, M.López Trascasa, M.Noris, I.M.Ponce Castro, G.Remuzzi, S.Rodríguez de Córdoba, P.Sánchez-Corral, C.Skerka, P.F.Zipfel, and S.J.Perkins (2007).
The interactive Factor H-atypical hemolytic uremic syndrome mutation database and website: update and integration of membrane cofactor protein and Factor I mutations with structural models.

Hum Mutat, 28, 222-234.

17018530

J.E.Lee, and Y.Kim (2006).
A tissue-specific variant of the human lysyl oxidase-like protein 3 (LOXL3) functions as an amine oxidase with substrate specificity.

J Biol Chem, 281, 37282-37290.

16524885

Y.Chen, M.Sankala, J.R.Ojala, Y.Sun, A.Tuuttila, D.E.Isenman, K.Tryggvason, and T.Pikkarainen (2006).
A phage display screen and binding studies with acetylated low density lipoprotein provide evidence for the importance of the scavenger receptor cysteine-rich (SRCR) domain in the ligand-binding function of MARCO.

J Biol Chem, 281, 12767-12775.

15561712

C.W.Franzke, P.Bruckner, and L.Bruckner-Tuderman (2005).
Collagenous transmembrane proteins: recent insights into biology and pathology.

J Biol Chem, 280, 4005-4008.

16245330

M.A.Sarraj, P.J.McClive, H.P.Wilmore, K.L.Loveland, and A.H.Sinclair (2005).
Novel scavenger receptor gene is differentially expressed in the embryonic and adult mouse testis.

Dev Dyn, 234, 1026-1033.

16030018

M.R.Sarrias, S.Roselló, F.Sánchez-Barbero, J.M.Sierra, J.Vila, J.Yélamos, J.Vives, C.Casals, and F.Lozano (2005).
A role for human Sp alpha as a pattern recognition receptor.

J Biol Chem, 280, 35391-35398.

15188432

A.Schmidt, D.Wenzel, I.Ferring, S.Kazemi, T.Sasaki, J.Hescheler, R.Timpl, K.Addicks, B.K.Fleischmann, and W.Bloch (2004).
Influence of endostatin on embryonic vasculo- and angiogenesis.

Dev Dyn, 230, 468-480.

15292166

I.Boulatnikov, and R.C.De Lisle (2004).
Binding of the Golgi sorting receptor muclin to pancreatic zymogens through sulfated O-linked oligosaccharides.

J Biol Chem, 279, 40918-40926.

15448162

M.Madsen, H.J.Møller, M.J.Nielsen, C.Jacobsen, J.H.Graversen, T.van den Berg, and S.K.Moestrup (2004).
Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region.

J Biol Chem, 279, 51561-51567.

15009805

M.R.Sarrias, O.Padilla, Y.Monreal, M.Carrascal, J.Abian, J.Vives, J.Yélamos, and F.Lozano (2004).
Biochemical characterization of recombinant and circulating human Spalpha.

Tissue Antigens, 63, 335-344.

15242536

Z.Wu, E.Golub, W.R.Abrams, and D.Malamud (2004).
gp340 (SAG) binds to the V3 sequence of gp120 important for chemokine receptor interaction.

AIDS Res Hum Retroviruses, 20, 600-607.

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.

12962630

J.R.Somoza, J.D.Ho, C.Luong, M.Ghate, P.A.Sprengeler, K.Mortara, W.D.Shrader, D.Sperandio, H.Chan, M.E.McGrath, and B.A.Katz (2003).
The structure of the extracellular region of human hepsin reveals a serine protease domain and a novel scavenger receptor cysteine-rich (SRCR) domain.

Structure, 11, 1123-1131.

PDB code:

1p57

14551188

M.S.Kim, S.S.Kim, S.T.Jung, J.Y.Park, H.W.Yoo, J.Ko, K.Csiszar, S.Y.Choi, and Y.Kim (2003).
Expression and purification of enzymatically active forms of the human lysyl oxidase-like protein 4.

J Biol Chem, 278, 52071-52074.

12354219

C.Claudianos, J.T.Dessens, H.E.Trueman, M.Arai, J.Mendoza, G.A.Butcher, T.Crompton, and R.E.Sinden (2002).
A malaria scavenger receptor-like protein essential for parasite development.

Mol Microbiol, 45, 1473-1484.

12050164

F.J.Bikker, A.J.Ligtenberg, K.Nazmi, E.C.Veerman, W.van't Hof, J.G.Bolscher, A.Poustka, A.V.Nieuw Amerongen, and J.Mollenhauer (2002).
Identification of the bacteria-binding peptide domain on salivary agglutinin (gp-340/DMBT1), a member of the scavenger receptor cysteine-rich superfamily.

J Biol Chem, 277, 32109-32115.

11854028

J.H.Graversen, M.Madsen, and S.K.Moestrup (2002).
CD163: a signal receptor scavenging haptoglobin-hemoglobin complexes from plasma.

Int J Biochem Cell Biol, 34, 309-314.

12097327

M.Sankala, A.Brännström, T.Schulthess, U.Bergmann, E.Morgunova, J.Engel, K.Tryggvason, and T.Pikkarainen (2002).
Characterization of recombinant soluble macrophage scavenger receptor MARCO.

J Biol Chem, 277, 33378-33385.

11861604

R.Berland, and H.H.Wortis (2002).
Origins and functions of B-1 cells with notes on the role of CD5.

Annu Rev Immunol, 20, 253-300.

11867635

S.Hellstern, T.Sasaki, C.Fauser, A.Lustig, R.Timpl, and J.Engel (2002).
Functional studies on recombinant domains of Mac-2-binding protein.

J Biol Chem, 277, 15690-15696.

11378405

S.Gordon (2001).
Homeostasis: a scavenger receptor for haemoglobin.

Curr Biol, 11, R399-R401.

10861932

M.A.Bowen, A.A.Aruffo, and J.Bajorath (2000).
Cell surface receptors and their ligands: in vitro analysis of CD6-CD166 interactions.

Proteins, 40, 420-428.

10753817

M.C.Deller, and E.Yvonne Jones (2000).
Cell surface receptors.

Curr Opin Struct Biol, 10, 213-219.

10771511

S.Laferté, L.C.Loh, and V.Keeler (2000).
Monoclonal antibodies specific for human tumor-associated antigen 90K/Mac-2 binding protein: tools to examine protein conformation and function.

J Cell Biochem, 77, 540-559.

11069281

Z.Pancer (2000).
Dynamic expression of multiple scavenger receptor cysteine-rich genes in coelomocytes of the purple sea urchin.

Proc Natl Acad Sci U S A, 97, 13156-13161.

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.