2Q8O - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE GITR LIGAND DIMER

Authors :   Z. Zhaocai, T. Yukiko

Date :   11 Jun 07 (Deposition) - 25 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tnf, Gitr, Dimer, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhou, Y. Tone, X. Song, K. Furuuchi, J. D. Lear, H. Waldmann, M. Tone, M. I. Greene, R. Murali
Structural Basis For Ligand-Mediated Mouse Gitr Activation.
Proc. Natl. Acad. Sci. Usa V. 105 641 2008
PubMed-ID: 18178614 | Reference-DOI: 10.1073/PNAS.0711206105

Molecule 1 - GITR LIGAND
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	TNFSF18
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Q8O)

(no "Site" information available for 2Q8O)

Asymmetric/Biological Unit

No.	Residues
1	A:52	-	A:72
2	B:52	-	B:72

(no "Cis Peptide Bond" information available for 2Q8O)

(no "SAP(SNP)/Variant" information available for 2Q8O)

(no "PROSITE Motif" information available for 2Q8O)

(no "Exon" information available for 2Q8O)

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:125
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:125
                                    58        68        78        88        98       108       118       128       138       148       158       168     
          TNF18_MOUSE    49 IESCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d2q8oa1 A:49-173 Glucocorticoid-induced TNF-related ligand, TNFSF18                                                           SCOP domains
               CATH domains 2q8oA00 A:49-173  [code=2.60.120.40, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeee.......eee.....eee...eeeeeeeee...hhhhh.....eeeeeee..eeeeeeee....eeeeeeeee....eeeeee.hhhhh.....eeeeee.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8o A  49 IESCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKNNTYWGIILMPDLPFIS 173
                                    58        68        78        88        98       108       118       128       138       148       158       168

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:125
                                    58        68        78        88        98       108       118       128       138       148       158       168     
          TNF18_MOUSE    49 IESCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d2q8ob_ B: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                                 SCOP domains
               CATH domains 2q8oB00 B:49-173  [code=2.60.120.40, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeee.......eee.....eee...eeeeeeeee...hhhhh.....eeeeeee..eeeeeeee....ee..eeeee....eeeeee.hhhhh.....eeeeee.....eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8o B  49 IESCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKNNTYWGIILMPDLPFIS 173
                                    58        68        78        88        98       108       118       128       138       148       158       168

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: TNF-like (100)

Superfamily: TNF-like (100)

Family: TNF-like (82)

Protein domain: Glucocorticoid-induced TNF-related ligand, TNFSF18 (11)

Mouse (Mus musculus) [TaxId: 10090] (4)

1a	d2q8oa1	A:49-173
1b	d2q8ob_	B:

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.40, no name defined] (56)

House mouse (Mus musculus) (14)

1a	2q8oA00	A:49-173
1b	2q8oB00	B:49-173

(no "Pfam Domain" information available for 2Q8O)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TNF18_MOUSE | Q7TS55)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005164	tumor necrosis factor receptor binding	Interacting selectively and non-covalently with the tumor necrosis factor receptor.
	GO:0032813	tumor necrosis factor receptor superfamily binding	Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily.
biological process
	GO:0002309	T cell proliferation involved in immune response	The expansion of a T cell population by cell division as part of an immune response.
	GO:0035741	activated CD4-positive, alpha-beta T cell proliferation	The expansion of an activated CD4-positive, alpha-beta T cell population by cell division.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0032613	interleukin-10 production	The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0032615	interleukin-12 production	The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:2000329	negative regulation of T-helper 17 cell lineage commitment	Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 cell lineage commitment.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0002687	positive regulation of leukocyte migration	Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
	GO:0010759	positive regulation of macrophage chemotaxis	Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
	GO:0090026	positive regulation of monocyte chemotaxis	Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
	GO:0090073	positive regulation of protein homodimerization activity	Any process that increases the frequency, rate or extent of protein homodimerization, interacting selectively with an identical protein to form a homodimer.
	GO:2000348	regulation of CD40 signaling pathway	Any process that modulates the frequency, rate or extent of signaling via the CD40 signaling pathway.
	GO:0042129	regulation of T cell proliferation	Any process that modulates the frequency, rate or extent of T cell proliferation.
	GO:2000508	regulation of dendritic cell chemotaxis	Any process that modulates the frequency, rate or extent of dendritic cell chemotaxis.
	GO:0032649	regulation of interferon-gamma production	Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032675	regulation of interleukin-6 production	Any process that modulates the frequency, rate, or extent of interleukin-6 production.
	GO:0071637	regulation of monocyte chemotactic protein-1 production	Any process that modulates the frequency, rate, or extent of production of monocyte chemotactic protein-1.
	GO:0032680	regulation of tumor necrosis factor production	Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
	GO:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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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SS Bonds (2, 2)

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