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
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN4-1BB LIGAND ECTODOMAIN
 
Authors :  E. Y. Won, H. S. Cho
Date :  12 Jan 10  (Deposition) - 23 Mar 10  (Release) - 23 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Signal-Anchor, Cytokine, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Y. Won, K. Cha, J. S. Byun, D. U. Kim, S. Shin, B. Ahn, Y. H. Kim, A. J. Rice, T. Walz, B. S. Kwon, H. S. Cho
The Structure Of The Trimer Of Human 4-1Bb Ligand Is Unique Among Members Of The Tumor Necrosis Factor Superfamily.
J. Biol. Chem. V. 285 9202 2010
PubMed-ID: 20032458  |  Reference-DOI: 10.1074/JBC.M109.084442

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 80-246
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym4-1BB LIGAND, 4-1BBL

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2X29)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X29)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Mse A:168 -Pro A:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X29)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNFL9_HUMAN93-240  1A:93-240
2TNF_1PS00251 TNF family signature.TNFL9_HUMAN133-149  1A:133-149
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.TNFL9_HUMAN93-240  3A:93-240
2TNF_1PS00251 TNF family signature.TNFL9_HUMAN133-149  3A:133-149

(-) Exons   (0, 0)

(no "Exon" information available for 2X29)

(-) 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:156
 aligned with TNFL9_HUMAN | P41273 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:167
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
          TNFL9_HUMAN    80 DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPA 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------TNF-2x29A01 A:107-240                                                                                                                 ------ Pfam domains
         Sec.struct. author ...eee......eeeeee.......ee..ee......................eee...eeeeeeeeeeeee.......eeeeeeeeee.------...eeeeeee..-----..eeeeeeeeeeee...eeeeeeee.hhhhhh.eee.....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------TNF_2  PDB: A:93-240 UniProt: 93-240                                                                                                                ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------TNF_1            ------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x29 A  80 DPAGLLDLRQGmFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQmELRRVVAGEGSGSVSLALHLmP------AAALALTVDLPP-----RNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPA 246
                                    89 |      99       109       119       129       139       149       159       169      |179       | -   |   199       209       219       229       239       
                                      91-MSE                                                 147-MSE              168-MSE 176        187   193                                                     
                                                                                                                   169                                                                             

   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  (0, 0)

(no "SCOP Domain" information available for 2X29)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X29)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C1q_TNF (45)
(-)
Family: TNF (37)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNFL9_HUMAN | P41273)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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: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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0043011    myeloid dendritic cell differentiation    The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
    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:0045585    positive regulation of cytotoxic T cell differentiation    Any process that activates or increases the frequency, rate or extent of cytotoxic T cell differentiation.
    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:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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.
cellular component
    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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2x29)
 
  Cis Peptide Bonds
    Mse A:168 - Pro A:169   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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
  2x29
    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
  TNFL9_HUMAN | P41273
    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
  TNFL9_HUMAN | P41273
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2X29)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2X29)