2QDN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE GITRL

Authors :   K. Chattopadhyay, U. A. Ramagopal, S. G. Nathenson, S. C. Almo

Date :   21 Jun 07 (Deposition) - 01 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Gitrl; Glucocorticoid-Induced Tnf Receptor Ligand, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Chattopadhyay, U. A. Ramagopal, M. Brenowitz, S. G. Nathenson, S. C. Almo
Evolution Of Gitrl Immune Function: Murine Gitrl Exhibits Unique Structural And Biochemical Properties Within The Tnf Superfamily.
Proc. Natl. Acad. Sci. Usa V. 105 635 2008
PubMed-ID: 18182486 | Reference-DOI: 10.1073/PNAS.0710529105

Molecule 1 - GITR LIGAND
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Fragment	:	TNF HOMOLOGY DOMAIN (RESIDUES 46-173)
	Gene	:	GITRL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	GLUCOCORTICOID-INDUCED-TUMOR NECROSIS FACTOR RECEPTOR LIGAND

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2QDN)

Asymmetric/Biological Unit

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

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

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

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

(no "Exon" information available for 2QDN)

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:123
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:123
                                    60        70        80        90       100       110       120       130       140       150       160       170   
          TNF18_MOUSE    51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d2qdna1 A:51-173 Glucocorticoid-induced TNF-related ligand, TNFSF18                                                         SCOP domains
               CATH domains 2qdnA00 A:51-173  [code=2.60.120.40, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee.......eee.....eee...eeeeeeeeeee.hhhhh.....eeeeeee..eeeeeeee....ee..eeeee....eeeeee.hhh.eeeeeeeeeeee.....eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdn A  51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
                                    60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with TNF18_MOUSE | Q7TS55 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:123
                                    60        70        80        90       100       110       120       130       140       150       160       170   
          TNF18_MOUSE    51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
               SCOP domains d2qdnb_ B: Glucocorticoid-induced TNF-related ligand, TNFSF18                                                               SCOP domains
               CATH domains 2qdnB00 B:51-173  [code=2.60.120.40, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee.......eee.....eee...eeeeeeeee...hhhhh......eeeeee..eeeeeee.....eeeeeeeee....eeeeee.hhhhh.....eeeeee.....eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdn B  51 SCMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVVQIYKKNDVLQTLMNDFQILPIGGVYELHAGDNIYLKFNSKDHIQKTNTYWGIILMPDLPFIS 173
                                    60        70        80        90       100       110       120       130       140       150       160       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: 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	d2qdna1	A:51-173
1b	d2qdnb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	2qdnA00	A:51-173
1b	2qdnB00	B:51-173

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

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.

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
(no "Ligands, Modified Residues, Ions" information available for 2qdn)

	Sites
(no "Sites" information available for 2qdn)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qdn)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2qdn
		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
	TNF18_MOUSE \| Q7TS55
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TNF18_MOUSE \| Q7TS55
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TNF18_MOUSE \| Q7TS55	:	2q8o 3b9i 3fc0

(no "Related Entries Specified in the PDB File" available for 2QDN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (33, 33)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File