1S55 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MOUSE RANKL STRUCTURE AT 1.9A RESOLUTION

Authors :   M. J. Teale, X. Feug, L. Chen, T. Bice, E. J. Meehan

Date :   19 Jan 04 (Deposition) - 05 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   M. J. Teale, N. Schorman, X. Feug, T. Bice, E. J. Meehan, L. Delucas
Murine Rankl Extra Cellular Domain Homotrimer Structure In Space Groups P212121 And H3 At 1. 9 And 2. 6 Respectively
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PGEX-4T-1
	Fragment	:	RESIDUES 161-316
	Gene	:	TNFSF11, RANKL, TRANCE, OPGL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND, RANKL, TNF-RELATED ACTIVATION-INDUCED CYTOKINE, TRANCE, OSTEOPROTEGERIN LIGAND, OPGL, OSTEOCLAST DIFFERENTIATION FACTOR, ODF, OSTEOCLASTOGENESIS-INHIBITORY FACTOR, OCIF

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:194 , LYS C:281	BINDING SITE FOR RESIDUE CL A 317
2	AC2	SOFTWARE	LYS B:281 , LYS C:194	BINDING SITE FOR RESIDUE CL B 317
3	AC3	SOFTWARE	LYS A:281 , LYS B:194	BINDING SITE FOR RESIDUE CL A 318

(no "SS Bond" information available for 1S55)

(no "Cis Peptide Bond" information available for 1S55)

(no "SAP(SNP)/Variant" information available for 1S55)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TNF11_MOUSE	165-312	3	A:165-312 B:165-312 C:165-312

(no "Exon" information available for 1S55)

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:156
 aligned with TNF11_MOUSE | O35235 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:156
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      
          TNF11_MOUSE   161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
               SCOP domains d1s55a_ A: TRANCE/RANKL cytokine                                                                                                                             SCOP domains
               CATH domains 1s55A00 A:161-316  [code=2.60.120.40, no name defined]                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...........ee...ee......eee.eeee..eeee...eeeeeeeeeeeeee.hhh.....eeeeeeeeeeee.....eeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: A:165-312 UniProt: 165-312                                                                                                              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s55 A 161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with TNF11_MOUSE | O35235 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:156
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      
          TNF11_MOUSE   161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
               SCOP domains d1s55b_ B: TRANCE/RANKL cytokine                                                                                                                             SCOP domains
               CATH domains 1s55B00 B:161-316  [code=2.60.120.40, no name defined]                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...........eee..ee......eee..ee....ee....eeeeeeeeeeeeee..........eeeeeeeeee.......eeeeeeeeee.......eeeeeeeeeeeeee....eeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: B:165-312 UniProt: 165-312                                                                                                              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s55 B 161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with TNF11_MOUSE | O35235 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:156
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310      
          TNF11_MOUSE   161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
               SCOP domains d1s55c_ C: TRANCE/RANKL cytokine                                                                                                                             SCOP domains
               CATH domains 1s55C00 C:161-316  [code=2.60.120.40, no name defined]                                                                                                       CATH domains
           Pfam domains (1) -----------------------TNF-1s55C01 C:184-312                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) -----------------------TNF-1s55C02 C:184-312                                                                                                            ---- Pfam domains (2)
           Pfam domains (3) -----------------------TNF-1s55C03 C:184-312                                                                                                            ---- Pfam domains (3)
         Sec.struct. author ...eeeeee.hhhh......eee..ee......eee..ee....ee....eeeeeeeeeeeeee.hhh.....eeeeeeeeeee.......eeeeeeeeeee......eeeeeeeeeeeeee....eeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: C:165-312 UniProt: 165-312                                                                                                              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s55 C 161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

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: TRANCE/RANKL cytokine (5)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d1s55a_	A:
1b	d1s55b_	B:
1c	d1s55c_	C:

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	1s55A00	A:161-316
1b	1s55B00	B:161-316
1c	1s55C00	C:161-316

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C1q_TNF (45)

Family: TNF (37)

Mus musculus (Mouse) (11)

1a	TNF-1s55C01	C:184-312
1b	TNF-1s55C02	C:184-312
1c	TNF-1s55C03	C:184-312

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (TNF11_MOUSE | O35235)

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: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:0048535	lymph node development	The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
	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: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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