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Title :   THE X-RAY CRYSTAL STRUCTURE OF MURINE OX40L

Authors :   S. G. Hymowitz, D. M. Compaan

Date :   22 Jun 06 (Deposition) - 29 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

Chains :   Asym. Unit : F
Biol. Unit 1: F  (3x)

Keywords :   Trimer, Tnfsf, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Compaan, S. G. Hymowitz
The Crystal Structure Of The Costimulatory Ox40-Ox40L Complex.
Structure V. 14 1321 2006
PubMed-ID: 16905106 | Reference-DOI: 10.1016/J.STR.2006.06.015

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 4
	Chains	:	F
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Strain	:	HI5
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN (RESIDUES 51-198)
	Gene	:	TNFSF4, OX40L, TXGP1L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	OX40 LIGAND, OX40L, CD252 ANTIGEN

		1
Asymmetric Unit	:	F
Biological Unit 1 (3x)	:	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN F:91	BINDING SITE FOR RESIDUE NAG F 200
2	AC2	SOFTWARE	ARG F:64 , LYS F:81 , ASN F:82 , ARG F:121 , HIS F:124	BINDING SITE FOR RESIDUE SO4 F 201

Asymmetric Unit

No.	Residues
1	F:70	-	F:163
2	F:98	-	F:183

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_1	PS00251	TNF family signature.	TNFL4_MOUSE	94-110	1	F:94-110

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_1	PS00251	TNF family signature.	TNFL4_MOUSE	94-110	3	F:94-110

(no "Exon" information available for 2HEW)

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 F from PDB  Type:PROTEIN  Length:128
 aligned with TNFL4_MOUSE | P43488 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:128
                                    67        77        87        97       107       117       127       137       147       157       167       177        
          TNFL4_MOUSE    58 PPIQRLRGAVTRCEDGQLFISSYKNEYQTMEVQNNSVVIKCDGLYIIYLKGSFFQEVKIDLHFREDHNPISIPMLNDGRRIVFTVVASLAFKDKVYLTVNAPDTLCEHLQINDGELIVVQLTPGYCAP 185
               SCOP domains d2hewf1 F:58-185 Tumor necrosis factor ligand superfamily member 4, OX40L                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeee.........eee..eee....eeeeeeeeeee.....eeee.......eee.......eeeeeeeeee....eeeeee..hhhhhhhh.eeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------TNF_1            --------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hew F  58 PPIQRLRGAVTRCEDGQLFISSYKNEYQTMEVQNNSVVIKCDGLYIIYLKGSFFQEVKIDLHFREDHNPISIPMLNDGRRIVFTVVASLAFKDKVYLTVNAPDTLCEHLQINDGELIVVQLTPGYCAP 185
                                    67        77        87        97       107       117       127       137       147       157       167       177

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 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: Tumor necrosis factor ligand superfamily member 4, OX40L (3)

Mouse (Mus musculus) [TaxId: 10090] (2)

d2hewf1

F:58-185

(no "CATH Domain" information available for 2HEW)

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

Asymmetric Unit(hide GO term definitions)

Chain F (TNFL4_MOUSE | P43488)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	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:0035783	CD4-positive, alpha-beta T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment CD4-positive, alpha-beta T cell activation.
	GO:0042098	T cell proliferation	The expansion of a T cell population by cell division. Follows T cell activation.
	GO:0035712	T-helper 2 cell activation	The change in morphology and behavior of a T helper 2 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0002526	acute inflammatory response	Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
	GO:0001568	blood vessel development	The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0035714	cellular response to nitrogen dioxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen dioxide (NO2) stimulus.
	GO:0071380	cellular response to prostaglandin E stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a prostagladin E stimulus.
	GO:0071954	chemokine (C-C motif) ligand 11 production	The appearance of chemokine (C-C motif) ligand 11 (CCL11, also known as eotaxin-1) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0001816	cytokine production	The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0002215	defense response to nematode	A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	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:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0035709	memory T cell activation	The change in morphology and behavior of a memory T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0070233	negative regulation of T cell apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell death by apoptotic process.
	GO:0045626	negative regulation of T-helper 1 cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation.
	GO:0070236	negative regulation of activation-induced cell death of T cells	Any process that stops, prevents, or reduces the frequency, rate or extent of activation-induced cell death of T cells.
	GO:0050710	negative regulation of cytokine secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell.
	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
	GO:0032689	negative regulation of interferon-gamma production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032700	negative regulation of interleukin-17 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
	GO:0045590	negative regulation of regulatory T cell differentiation	Any process that stops, prevents, or reduces the rate of differentiation of regulatory T cells.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
	GO:1900281	positive regulation of CD4-positive, alpha-beta T cell costimulation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell costimulation.
	GO:0043372	positive regulation of CD4-positive, alpha-beta T cell differentiation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell differentiation.
	GO:2000525	positive regulation of T cell costimulation	Any process that activates or increases the frequency, rate or extent of T cell costimulation.
	GO:0002726	positive regulation of T cell cytokine production	Any process that activates or increases the frequency, rate, or extent of T cell cytokine production.
	GO:2000406	positive regulation of T cell migration	Any process that activates or increases the frequency, rate or extent of T cell migration.
	GO:2000570	positive regulation of T-helper 2 cell activation	Any process that activates or increases the frequency, rate or extent of T-helper 2 cell activation.
	GO:0045630	positive regulation of T-helper 2 cell differentiation	Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation.
	GO:0042104	positive regulation of activated T cell proliferation	Any process that activates or increases the rate or extent of activated T cell proliferation.
	GO:0046641	positive regulation of alpha-beta T cell proliferation	Any process that activates or increases the frequency, rate or extent of alpha-beta T cell proliferation.
	GO:0002699	positive regulation of immune effector process	Any process that activates or increases the frequency, rate, or extent of an immune effector process.
	GO:0002891	positive regulation of immunoglobulin mediated immune response	Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response.
	GO:0051024	positive regulation of immunoglobulin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032733	positive regulation of interleukin-10 production	Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
	GO:0032735	positive regulation of interleukin-12 production	Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
	GO:0032736	positive regulation of interleukin-13 production	Any process that activates or increases the frequency, rate, or extent of interleukin-13 production.
	GO:0032743	positive regulation of interleukin-2 production	Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
	GO:0032753	positive regulation of interleukin-4 production	Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
	GO:2000572	positive regulation of interleukin-4-dependent isotype switching to IgE isotypes	Any process that activates or increases the frequency, rate or extent of interleukin-4-dependent isotype switching to IgE isotypes.
	GO:0032755	positive regulation of interleukin-6 production	Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
	GO:2000568	positive regulation of memory T cell activation	Any process that activates or increases the frequency, rate or extent of memory T cell activation.
	GO:0043382	positive regulation of memory T cell differentiation	Any process that activates or increases the frequency, rate or extent of memory T cell differentiation.
	GO:0002830	positive regulation of type 2 immune response	Any process that activates or increases the frequency, rate, or extent of a type 2 immune response.
	GO:0002819	regulation of adaptive immune response	Any process that modulates the frequency, rate, or extent of an adaptive immune response.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:0035713	response to nitrogen dioxide	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen dioxide (NO2) stimulus.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
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.

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	2hew
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	TNFL4_MOUSE \| P43488
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	TNFL4_MOUSE \| P43488	:	2hey

Description

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Ligands, Modified Residues, Ions (2, 2)

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SS Bonds (2, 2)

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