2OYA - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE DIMERIC FORM OF THE SRCR DOMAIN OF MOUSE MARCO

Authors :   J. R. M. Ojala, T. Pikkarainen, A. Tuuttila, T. Sandalova, K. Tryggvaso

Date :   21 Feb 07 (Deposition) - 17 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Extracellular Matrix, Scavenger Receptor Cysteine-Rich (Srcr), Macrophage Receptor, Ligand Binding, Basic Cluster, Acidic Cluster, Sulfate Binding, Dimer, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Ojala, T. Pikkarainen, A. Tuuttila, T. Sandalova, K. Tryggvason
Crystal Structure Of The Cysteine-Rich Domain Of Scavenger Receptor Marco Reveals The Presence Of A Basic And An Acidi Cluster That Both Contribute To Ligand Recognition.
J. Biol. Chem. V. 282 16654 2007
PubMed-ID: 17405873 | Reference-DOI: 10.1074/JBC.M701750200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRCR_2	PS50287	SRCR domain profile.	MARCO_MOUSE	423-518	2	A:423-518 B:423-518
2	SRCR_1	PS00420	SRCR domain signature.	MARCO_MOUSE	426-463	2	A:426-463 B:426-463

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRCR_2	PS50287	SRCR domain profile.	MARCO_MOUSE	423-518	1	A:423-518 -
2	SRCR_1	PS00420	SRCR domain signature.	MARCO_MOUSE	426-463	1	A:426-463 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRCR_2	PS50287	SRCR domain profile.	MARCO_MOUSE	423-518	1	- B:423-518
2	SRCR_1	PS00420	SRCR domain signature.	MARCO_MOUSE	426-463	1	- B:426-463

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRCR_2	PS50287	SRCR domain profile.	MARCO_MOUSE	423-518	2	A:423-518 B:423-518
2	SRCR_1	PS00420	SRCR domain signature.	MARCO_MOUSE	426-463	2	A:426-463 B:426-463

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:102
 aligned with MARCO_MOUSE | Q60754 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:140
                                   388       398       408       418       428       438       448       458       468       478       488       498       508       518
          MARCO_MOUSE   379 SPGLAGPKGEPGRVGQKGDPGMKGSSGQQGQKGEKGQKGESFQRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o ya                                     A00 A:417-518 Mac-2 Binding Protein;                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h-hh-------------------------------------h.eeeeeeeeeeeeeeee..eeeee.....hhhhhhhhhhhh...eeeee.........eee..........hhhhh..........hhhhh.eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------SRCR_2  PDB: A:423-518 UniProt: 423-518                                                          PROSITE (1)
                PROSITE (2) -----------------------------------------------SRCR_1  PDB: A:426-463                ------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oya A 417 AP-LA-------------------------------------QRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
                             | ||    -         -         -         -  |    428       438       448       458       468       478       488       498       508       518
                             | ||                                   421                                                                                                 
                           418 ||                                                                                                                                       
                             419|                                                                                                                                       
                              420

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with MARCO_MOUSE | Q60754 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:140
                                   388       398       408       418       428       438       448       458       468       478       488       498       508       518
          MARCO_MOUSE   379 SPGLAGPKGEPGRVGQKGDPGMKGSSGQQGQKGEKGQKGESFQRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o ya                                     B00 B:417-518 Mac-2 Binding Protein;                                                               CATH domains
           Pfam domains (1) -----------------------------------------------SRCR-2oyaB01 B:426-518                                                                        Pfam domains (1)
           Pfam domains (2) -----------------------------------------------SRCR-2oyaB02 B:426-518                                                                        Pfam domains (2)
         Sec.struct. author .h-hh-------------------------------------h.eeeeeeeeeeeeeeee..eeeee.....hhhhhhhhhhhh...eeeee.........eee..........hhhhh..........hhhhh.eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------SRCR_2  PDB: B:423-518 UniProt: 423-518                                                          PROSITE (1)
                PROSITE (2) -----------------------------------------------SRCR_1  PDB: B:426-463                ------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oya B 417 AP-LA-------------------------------------QRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
                             | ||    -         -         -         -  |    428       438       448       458       468       478       488       498       508       518
                           418 ||                                   421                                                                                                 
                             419|                                                                                                                                       
                              420

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MARCO_MOUSE | Q60754)

molecular function
	GO:0005044	scavenger receptor activity	Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
biological process
	GO:0043277	apoptotic cell clearance	The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
	GO:0005581	collagen trimer	A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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