3MJ6 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE GAMMADELTA T CELL COSTIMULATORY RECEPTOR JUNCTIONAL ADHESION MOLECULE-LIKE PROTEIN, JAML

Authors :   P. Verdino, I. A. Wilson

Date :   12 Apr 10 (Deposition) - 22 Sep 10 (Release) - 22 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A

Keywords :   Immunoglobulin Tandem Domain, Cell Adhesion, Cell Junction, Glycoprotein, Immunoglobulin Domain, Membrane, Costimulation, Transmembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Verdino, D. A. Witherden, W. L. Havran, I. A. Wilson
The Molecular Interaction Of Car And Jaml Recruits The Central Cell Signal Transducer Pi3K.
Science V. 329 1210 2010
PubMed-ID: 20813955 | Reference-DOI: 10.1126/SCIENCE.1187996
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:59	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	ASN A:69 , HIS A:72 , HOH A:642	BINDING SITE FOR RESIDUE NAG A 401
03	AC3	SOFTWARE	ASN A:105 , FUC A:502 , HOH A:644	BINDING SITE FOR RESIDUE NAG A 501
04	AC4	SOFTWARE	THR A:143 , GLU A:144 , NAG A:501 , HOH A:644	BINDING SITE FOR RESIDUE FUC A 502
05	AC5	SOFTWARE	VAL A:35 , TYR A:56 , ASN A:59 , HOH A:609 , HOH A:610 , HOH A:611	BINDING SITE FOR RESIDUE NA A 503
06	AC6	SOFTWARE	SER A:157 , GLY A:158 , PHE A:178 , GLN A:211	BINDING SITE FOR RESIDUE FMT A 601
07	AC7	SOFTWARE	SER A:168 , MET A:173 , GLY A:176	BINDING SITE FOR RESIDUE FMT A 602
08	AC8	SOFTWARE	SER A:43 , LYS A:44 , ASP A:47 , ALA A:49 , GLU A:51	BINDING SITE FOR RESIDUE FMT A 604
09	AC9	SOFTWARE	LYS A:91 , PRO A:120	BINDING SITE FOR RESIDUE FMT A 605
10	BC1	SOFTWARE	LYS A:33 , HIS A:34 , LYS A:104	BINDING SITE FOR RESIDUE FMT A 606
11	BC2	SOFTWARE	GLU A:94 , GLY A:95 , LEU A:116 , TRP A:117	BINDING SITE FOR RESIDUE FMT A 607
12	BC3	SOFTWARE	GLU A:51 , TYR A:52 , ARG A:127 , VAL A:128 , THR A:134 , HOH A:645	BINDING SITE FOR RESIDUE FMT A 608

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:227
 aligned with JAML_MOUSE | Q80UL9 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:227
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           JAML_MOUSE    30 SPQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPKDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQD 256
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee...........eeeeeeeee.......eeeeeee..eeee.hhhh..eee..........eee...hhhhheeeeeeeee.....eeeeeeeeeee.....eeeee....eee....ee.......eeeeeee.......eeeeeee......eee........eee..hhhhh...eee...hhhhheeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mj6 A  10 SPQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPRDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQD 236
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (JAML_MOUSE | Q80UL9)

molecular function
	GO:0050839	cell adhesion molecule binding	Interacting selectively and non-covalently with a cell adhesion molecule.
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0046629	gamma-delta T cell activation	The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0007157	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
	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:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0035696	monocyte extravasation	The migration of a monocyte from the blood vessels into the surrounding tissue.
	GO:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0072672	neutrophil extravasation	The migration of a neutrophil from the blood vessels into the surrounding tissue.
	GO:0060054	positive regulation of epithelial cell proliferation involved in wound healing	Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
cellular component
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mj6)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3mj6
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	JAML_MOUSE \| Q80UL9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description