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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF JAML IN COMPLEX WITH THE STIMULATORY ANTIBODY HL4E10

Authors :   P. Verdino, I. A. Wilson

Date :   12 Apr 10 (Deposition) - 23 Feb 11 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym./Biol. Unit : A,H,L

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

Reference :   P. Verdino, D. A. Witherden, M. S. Ferguson, A. L. Corper, A. Schiefner W. L. Havran, I. A. Wilson
Molecular Insights Into Gamma Delta T Cell Costimulation By An Anti-Jaml Antibody.
Structure V. 19 80 2011
PubMed-ID: 21220118 | Reference-DOI: 10.1016/J.STR.2010.10.007

Molecule 1 - JUNCTIONAL ADHESION MOLECULE-LIKE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PMT/BIP/V5-HIS A
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280)
	Gene	:	AMICA1, GM638, JAML
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	DENDRITIC CELL-SPECIFIC PROTEIN CREA7, MCREA7

Molecule 2 - STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
	Chains	:	L
	Organism Common	:	ARMENIAN HAMSTER
	Organism Scientific	:	CRICETULUS MIGRATORIUS
	Organism Taxid	:	10032
	Other Details	:	HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
	Strain	:	HYBRIDOMA

Molecule 3 - STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
	Chains	:	H
	Organism Common	:	ARMENIAN HAMSTER
	Organism Scientific	:	CRICETULUS MIGRATORIUS
	Organism Taxid	:	10032
	Other Details	:	HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
	Strain	:	HYBRIDOMA

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:59 , PHE A:78 , SER L:63	BINDING SITE FOR RESIDUE NAG A 301
2	AC2	SOFTWARE	ASN A:69 , GLN A:87	BINDING SITE FOR RESIDUE NAG A 401
3	AC3	SOFTWARE	PRO A:11 , GLN A:12 , LEU A:103 , ASN A:105 , NAG A:502 , FUC A:506	BINDING SITE FOR RESIDUE NAG A 501
4	AC4	SOFTWARE	SER A:10 , GLN A:12 , ARG A:14 , VAL A:27 , NAG A:501 , BMA A:503 , MAN A:504	BINDING SITE FOR RESIDUE NAG A 502
5	AC5	SOFTWARE	NAG A:502 , MAN A:504 , MAN A:505	BINDING SITE FOR RESIDUE BMA A 503
6	AC6	SOFTWARE	ARG A:14 , NAG A:502 , BMA A:503	BINDING SITE FOR RESIDUE MAN A 504
7	AC7	SOFTWARE	VAL A:8 , SER A:9 , BMA A:503	BINDING SITE FOR RESIDUE MAN A 505
8	AC8	SOFTWARE	VAL A:27 , GLN A:28 , THR A:30 , HIS A:34 , ASN A:80 , NAG A:501	BINDING SITE FOR RESIDUE FUC A 506

Asymmetric/Biological Unit

No.	Residues
1	A:25	-	A:99
2	A:138	-	A:216
3	H:22	-	H:92
4	H:142	-	H:208
5	L:23	-	L:88
6	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Tyr L:140	-	Pro L:141
2	Phe H:148	-	Pro H:149
3	Glu H:150	-	Pro H:151

(no "SAP(SNP)/Variant" information available for 3MJ9)

(no "PROSITE Motif" information available for 3MJ9)

(no "Exon" information available for 3MJ9)

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:229
 aligned with JAML_MOUSE | Q80UL9 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:229
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247         
          JAML_MOUSE     28 VSSPQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPKDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQD  256
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eee...........eeeeeeeee.......eeeeeee...eee.hhhh..eee..hhhhh...eee...hhhhheeeeeeeee....eee...eeeeee.....eeeee....eee....ee.......eeeeeee.......eeeeeee..........hhhhh..eee..hhhhh...eee...hhhhheeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj9 A    8 VSSPQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPRDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQD  236
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227

Chain H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee........eeeeeeee...........eeeee........eeeee....eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3mj9 H    1 QVQLKESGPGLLQPSQTLSLTCTVSGISLSDYGVHWVRQAPGKGLEWMGIIGHAGGTDYNSNLKSRVSISRDTSKSQVFLKLNSLQQEDTAMYFCARHFYTYFDVWGQGIQVTVSSATTTAPSVYPLAPANTVTLGCLVKGYFPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPG  228
                                    10        20        30        40        50        60        70        80  |||   87        97       107       117       127|      145       156||     171       183       193    |||206       216      |228
                                                                                                            82A||                                          127|               154|||    169|      180|            198||||               223|  
                                                                                                             82B|                                           136                156||     171       183             200|||                226  
                                                                                                              82C                                                               157|                                202||                     
                                                                                                                                                                                 162                                 203|                     
                                                                                                                                                                                                                      205

Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d3mj9l1 L:2-107 automated matches                                                                           d3mj9l2 L:108-212 automated matches                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.......eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eee..........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhh...eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj9 L    2 YTLTQPPLVSVALGQKATITCSGDKLSDVYVHWYQQKAGQAPVLVIYEDNRRPSGIPDHFSGSNSGNMATLTISKAQAGDEADYYCQSWDGTNSAWVFGSGTKVTVLGQPNAAPSVTLFPPSSEELKTNQATLVCMINGFYPADVAVTWEADGTPITQGVKTTQPSKSDSKYMATSYLTMTADAWKSRNTFICKVTHGGNTVEKSLSPS  212
                                   |12        22        32        42        52        62        72        82        92   ||  100      |109       119       129       139       149       159      |171       181       191       203         
                                   9|                                                                                  95A|        106A                                                         166||                           200|         
                                   11                                                                                   95B                                                                      168|                            203         
                                                                                                                                                                                                  170

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Cricetulus migratorius [TaxId: 10032] (5)

1a	d3mj9l1	L:2-107
1b	d3mj9l2	L:108-212

(no "CATH Domain" information available for 3MJ9)

(no "Pfam Domain" information available for 3MJ9)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	3mj9
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	JAML_MOUSE \| Q80UL9	:	3mj6 3mj7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (17, 17)

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