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Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN RANKL/OPG COMPLEX

Authors :   X. Q. Wang, X. D. Luan, Q. Y. Lu

Date :   22 Nov 11 (Deposition) - 11 Jul 12 (Release) - 11 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,Z
Biol. Unit 1: A,Z  (3x)

Keywords :   Cystein-Rich Domain, Beta-Sandwich, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. D. Luan, Q. Y. Lu, Y. N. Jiang, S. Y. Zhang, Q. Wang, H. H. Yuan, W. M. Zhao, J. W. Wang, X. Q. Wang
Crystal Structure Of Human Rankl Complexed With Its Decoy Receptor Osteoprotegerin
J. Immunol. V. 189 245 2012
PubMed-ID: 22664871 | Reference-DOI: 10.4049/JIMMUNOL.1103387

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11, SOLUBLE FORM
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 162-317
	Gene	:	TNFSF11, OPGL, RANKL, TRANCE
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	OSTEOCLAST DIFFERENTIATION FACTOR, ODF, OSTEOPROTEGERIN LIGAND, OPGL, RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, RANKL, TNF-RELATED ACTIVATION-INDUCED CYTOKINE, TRANCE

Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11B
	Chains	:	Z
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 22-186
	Gene	:	TNFRSF11B, OCIF, OPG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	OSTEOCLASTOGENESIS INHIBITORY FACTOR, OSTEOPROTEGERIN

		1	2
Asymmetric Unit	:	A	Z
Biological Unit 1 (3x)	:	A	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (1, 3)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN Z:157 , THR Z:159 , HOH Z:310	BINDING SITE FOR RESIDUE NAG Z 201

Asymmetric Unit

No.	Residues
1	Z:20	-	Z:33
2	Z:23	-	Z:41
3	Z:44	-	Z:59
4	Z:62	-	Z:76
5	Z:66	-	Z:84
6	Z:86	-	Z:97
7	Z:103	-	Z:121
8	Z:124	-	Z:139
9	Z:145	-	Z:164

Asymmetric Unit

No.	Residues
1	Ser Z:63	-	Pro Z:64

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018957	V	104	M	TR11B_HUMAN	Polymorphism	11573906	Z	V	83	M
2	UniProt	VAR_037424	M	199	K	TNF11_HUMAN	Disease (OPTB2)	121909072	A	M	199	K

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018957	V	104	M	TR11B_HUMAN	Polymorphism	11573906	Z	V	83	M
2	UniProt	VAR_037424	M	199	K	TNF11_HUMAN	Disease (OPTB2)	121909072	A	M	199	K

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TR11B_HUMAN	62-105	1	Z:41-84
2	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TR11B_HUMAN	64-105 106-142	2	Z:43-84 Z:85-121
3	TNF_2	PS50049	TNF family profile.	TNF11_HUMAN	166-313	1	A:166-313

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNFR_NGFR_1	PS00652	TNFR/NGFR family cysteine-rich region signature.	TR11B_HUMAN	62-105	3	Z:41-84
2	TNFR_NGFR_2	PS50050	TNFR/NGFR family cysteine-rich region domain profile.	TR11B_HUMAN	64-105 106-142	6	Z:43-84 Z:85-121
3	TNF_2	PS50049	TNF family profile.	TNF11_HUMAN	166-313	3	A:166-313

(no "Exon" information available for 3URF)

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 A from PDB  Type:PROTEIN  Length:156
 aligned with TNF11_HUMAN | O14788 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:156
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      
          TNF11_HUMAN   162 AQPFAHLTINATDIPSGSHKVSLSSWYHDRGWAKISNMTFSNGKLIVNQDGFYYLYANICFRHHETSGDLATEYLQLMVYVTKTSIKIPSSHTLMKGGSTKYWSGNSEFHFYSINVGGFFKLRSGEEISIEVSNPSLLDPDQDATYFGAFKVRDID 317
               SCOP domains d3urfa_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...........eee..ee......eee.eeee..eeee...eeeeeeeeeeeeee.........eeeeeeeeeeee......eeeeeeeeeee......eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------K---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: A:166-313 UniProt: 166-313                                                                                                              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3urf A 162 AQPFAHLTINATDIPSGSHKVSLSSWYHDRGWAKISNMTFSNGKLIVNQDGFYYLYANICFRHHETSGDLATEYLQLMVYVTKTSIKIPSSHTLMKGGSTKYWSGNSEFHFYSINVGGFFKLRSGEEISIEVSNPSLLDPDQDATYFGAFKVRDID 317
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain Z from PDB  Type:PROTEIN  Length:164
 aligned with TR11B_HUMAN | O00300 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:164
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
          TR11B_HUMAN    26 PKYLHYDEETSHQLLCDKCPPGTYLKQHCTAKWKTVCAPCPDHYYTDSWHTSDECLYCSPVCKELQYVKQECNRTHNRVCECKEGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSGNS 189
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee........eee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee.......eeeee........eeee....ee..........ee........................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------M------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------TNFR_NGFR_1  PDB: Z:41-84 UniProt: 62-105   TNFR_NGFR_2  PDB: Z:85-121           ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------TNFR_NGFR_2  PDB: Z:43-84 UniProt: 64-105 ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3urf Z   5 PKYLHYDEETSHQLLCDKCPPGTYLKQHCTAKWKTVCAPCPDHYYTDSWHTSDECLYCSPVCKELQYVKQECNRTHNRVCECKEGRYLEIEFCLKHRSCPPGFGVVQAGTPERNTVCKRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNATHDNICSHHH 168
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164

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: automated matches (12)

Human (Homo sapiens) [TaxId: 9606] (8)

d3urfa_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (TNF11_HUMAN | O14788)

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:0070371	ERK1 and ERK2 cascade	An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0071847	TNFSF11-mediated signaling pathway	A series of molecular signals initiated by the binding of tumor necrosis factor ligand superfamily member 11 (TNFSF11) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007257	activation of JUN kinase activity	The initiation of the activity of the inactive enzyme JUN kinase (JNK).
	GO:0009887	animal organ morphogenesis	Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
	GO:0045453	bone resorption	The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
	GO:0055074	calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0060749	mammary gland alveolus development	The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
	GO:0033598	mammary gland epithelial cell proliferation	The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
	GO:0002548	monocyte chemotaxis	The movement of a monocyte in response to an external stimulus.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0030316	osteoclast differentiation	The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
	GO:0002158	osteoclast proliferation	The multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes.
	GO:0038001	paracrine signaling	The transfer of information from one cell to another, where the signal travels from the signal-producing cell to the receiving cell by passive diffusion or bulk flow in intercellular fluid. The signaling cell and the receiving cell are usually in the vicinity of each other.
	GO:0071848	positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling	Any TNFSF11-mediated signaling process that increases the rate, frequency, or extent of the ERK1 and ERK2 cascade.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	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:0050870	positive regulation of T cell activation	Any process that activates or increases the frequency, rate or extent of T cell activation.
	GO:0045780	positive regulation of bone resorption	Any process that activates or increases the frequency, rate or extent of bone resorption.
	GO:0051466	positive regulation of corticotropin-releasing hormone secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin-releasing hormone from a cell.
	GO:0071812	positive regulation of fever generation by positive regulation of prostaglandin secretion	Any process that increases the rate or extent of fever generation via positive regulation of the frequency, rate or extent of the regulated release of a prostaglandin from a cell.
	GO:0034112	positive regulation of homotypic cell-cell adhesion	Any process that activates or increases the frequency, rate, or extent of homotypic cell-cell adhesion.
	GO:1902533	positive regulation of intracellular signal transduction	Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
	GO:2001206	positive regulation of osteoclast development	Any process that activates or increases the frequency, rate or extent of osteoclast development.
	GO:0045672	positive regulation of osteoclast differentiation	Any process that activates or increases the frequency, rate or extent of osteoclast differentiation.
	GO:0042327	positive regulation of phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
	GO:0051897	positive regulation of protein kinase B signaling	Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0045670	regulation of osteoclast differentiation	Any process that modulates the frequency, rate or extent of osteoclast differentiation.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005887	integral component of plasma membrane	The component of the plasma 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.

Chain Z (TR11B_HUMAN | O00300)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0005031	tumor necrosis factor-activated receptor activity	Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	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:0045779	negative regulation of bone resorption	Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
	GO:0042489	negative regulation of odontogenesis of dentin-containing tooth	Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0046685	response to arsenic-containing substance	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 an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0043627	response to estrogen	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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
	GO:0010035	response to inorganic substance	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 an inorganic substance stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (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:0032026	response to magnesium ion	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 magnesium ion stimulus.
	GO:0007584	response to nutrient	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 nutrient stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005887	integral component of plasma membrane	The component of the plasma 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: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.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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		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
	TNF11_HUMAN \| O14788
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TR11B_HUMAN \| O00300
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TNF11_HUMAN \| O14788	:	5bnq

(no "Related Entries Specified in the PDB File" available for 3URF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (9, 9)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (3, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (68, 75)

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