Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF EXTRACELLULAR DOMAINS OF MOUSE RANK-RANKL COMPLEX
 
Authors :  H. M. Ta, G. T. T. Nguyen, H. M. Jin, J. K. Choi, H. Park, N. S. Kim, H. Y. Hwan
Date :  13 Jan 11  (Deposition) - 02 Mar 11  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Keywords :  Tumor Necrosis Factor (Tnf) Ligand-Receptor Superfamily Fold, Cytokine-Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. M. Ta, G. T. T. Nguyen, H. M. Jin, J. K. Choi, H. Park, N. S. Kim, H. Y. Hwang, K. K. Kim
Structure-Based Development Of A Receptor Activator Of Nuclear Factor-Kappab Ligand (Rankl) Inhibitor Peptide And Molecular Basis For Osteopetrosis
Proc. Natl. Acad. Sci. Usa V. 107 20281 2010
PubMed-ID: 21059944  |  Reference-DOI: 10.1073/PNAS.1011686107

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVFT3S
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 157-316
    GeneRANKL
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRANKL
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVFT3S
    Expression System StrainORIGAMI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 32-201
    GeneRANK
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRANK

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (3x)AB  
Biological Unit 2 (3x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3QBQ)

(-) Sites  (0, 0)

(no "Site" information available for 3QBQ)

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1B:35 -B:47
2B:48 -B:61
3B:51 -B:69
4B:72 -B:87
5B:93 -B:113
6B:115 -B:128
7B:125 -B:127
8B:134 -B:152
9B:155 -B:170
10B:176 -B:195
11D:35 -D:47
12D:48 -D:61
13D:51 -D:69
14D:72 -D:87
15D:93 -D:113
16D:115 -D:128
17D:125 -D:127
18D:134 -D:152
19D:155 -D:170
20D:176 -D:195

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His B:142 -Pro B:143
2His D:142 -Pro D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QBQ)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR11_MOUSE35-69
 
  2B:35-69
D:35-69
2TNF_2PS50049 TNF family profile.TNF11_MOUSE165-312
 
  2A:165-312
C:165-312
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR11_MOUSE35-69
 
  3B:35-69
-
2TNF_2PS50049 TNF family profile.TNF11_MOUSE165-312
 
  3A:165-312
-
Biological Unit 2 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR11_MOUSE35-69
 
  3-
D:35-69
2TNF_2PS50049 TNF family profile.TNF11_MOUSE165-312
 
  3-
C:165-312

(-) Exons   (0, 0)

(no "Exon" information available for 3QBQ)

(-) Sequences/Alignments

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:155
 aligned with TNF11_MOUSE | O35235 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:155
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
          TNF11_MOUSE   161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDI 315
               SCOP domains d3qbqa_ A: TRANCE/RANKL cytokine                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...........ee...ee......eee.eee....eee...eeeeeeeeeeeeee.hhh.......eeeeeeeeee..eeeeeeeeeeeee........eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: A:165-312 UniProt: 165-312                                                                                                              --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbq A 161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDI 315
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with TNR11_MOUSE | O35305 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:164
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
          TNR11_MOUSE    35 CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS 198
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee....eee.....eeeee........eeee....ee..........ee....hhhh.eeeee........eeee...eeee....eeee.......eee...........eee....ee..........ee..hhhhhh.eeee........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TNFR_NGFR_1  PDB: B:35-69          --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbq B  35 CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS 198
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with TNF11_MOUSE | O35235 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:155
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
          TNF11_MOUSE   161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDI 315
               SCOP domains d3qbqc_ C: TRANCE/RANKL cytokine                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------TNF-3qbqC01 C:184-312                                                                                                            --- Pfam domains (1)
           Pfam domains (2) -----------------------TNF-3qbqC02 C:184-312                                                                                                            --- Pfam domains (2)
         Sec.struct. author ...eeeeee.hhhh......ee...ee......eee.eeee..eeee...eeeeeeeeeeeeee.hhh.......eeeeeeeeee......eeeeeeeee........eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TNF_2  PDB: C:165-312 UniProt: 165-312                                                                                                              --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbq C 161 AQPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDI 315
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with TNR11_MOUSE | O35305 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:164
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
          TNR11_MOUSE    35 CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS 198
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TNFR_c6-3qbqD01 D:35-69            --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) TNFR_c6-3qbqD02 D:35-69            --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....................eeeee........eeee....ee..........ee....hhhh.eeeee........eeee...eeee....eeee.......eee...........eee....ee..........ee..hhhhhh.eeee........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TNFR_NGFR_1  PDB: D:35-69          --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbq D  35 CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS 198
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: TNF (37)
1aTNF-3qbqC01C:184-312
1bTNF-3qbqC02C:184-312

(-) Gene Ontology  (67, 83)

Asymmetric Unit(hide GO term definitions)
Chain A,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.

Chain B,D   (TNR11_MOUSE | O35305)
molecular function
    GO:0019955    cytokine binding    Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
    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: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: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: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:0060086    circadian temperature homeostasis    Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours.
    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: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: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:0043507    positive regulation of JUN kinase activity    Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
    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: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: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: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: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:0034097    response to cytokine    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 cytokine stimulus.
    GO:0070555    response to interleukin-1    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 interleukin-1 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:0009314    response to radiation    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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0034612    response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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 3qbq)
 
  Sites
(no "Sites" information available for 3qbq)
 
  Cis Peptide Bonds
    His B:142 - Pro B:143   [ RasMol ]  
    His D:142 - Pro D:143   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qbq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TNF11_MOUSE | O35235
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TNR11_MOUSE | O35305
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TNF11_MOUSE | O35235
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TNR11_MOUSE | O35305
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TNF11_MOUSE | O352351iqa 1jtz 1s55 3me2 4e4d 4giq
        TNR11_MOUSE | O353053me2 3me4 4giq 5bnq

(-) Related Entries Specified in the PDB File

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