Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF GRO(SLASH)MELANOMA GROWTH STIMULATORY ACTIVITY DETERMINED BY 1H NMR SPECTROSCOPY
 
Authors :  K. -S. Kim, I. Clark-Lewis, B. D. Sykes
Date :  25 Jan 95  (Deposition) - 31 Mar 95  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Cytokine (Chemotactic) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. S. Kim, I. Clark-Lewis, B. D. Sykes
Solution Structure Of Gro/Melanoma Growth Stimulatory Activity Determined By 1H Nmr Spectroscopy.
J. Biol. Chem. V. 269 32909 1994
PubMed-ID: 7806518
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN MELANOMA GROWTH STIMULATORY ACTIVITY
    ChainsA, B
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1MSG)

(-) Sites  (0, 0)

(no "Site" information available for 1MSG)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:9 -A:35
2A:11 -A:51

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.GROA_HUMAN43-87
 
  2A:9-53
B:9-53

(-) Exons   (3, 6)

NMR Structure (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003957611bENSE00002031450chr4:74735121-74735287167GROA_HUMAN1-34340--
1.2ENST000003957612ENSE00001746882chr4:74735386-74735509124GROA_HUMAN34-75422A:1-41
B:1-41
41
41
1.3aENST000003957613aENSE00001077828chr4:74735623-7473570684GROA_HUMAN75-103292A:41-69
B:41-69
29
29
1.4ENST000003957614ENSE00001785277chr4:74736238-74736959722GROA_HUMAN103-10752A:69-72
B:69-72
4
4

(-) Sequences/Alignments

NMR Structure
   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:72
 aligned with GROA_HUMAN | P09341 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:72
                                    44        54        64        74        84        94       104  
           GROA_HUMAN    35 ASVATELRCQCLQTLQGIHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNSDKS 106
               SCOP domains d1msga_ A: Melanoma growth stimulating activity (MGSA)                   SCOP domains
               CATH domains 1msgA00 A:1-72  [code=2.40.50.40, no name defined]                       CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................eeeee.........eeeee.....eee.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CXC  PDB: A:9-53             ------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-41 UniProt: 34-75     ---------------------------1.4  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3a  PDB: A:41-69      --- Transcript 1 (2)
                 1msg A   1 ASVATELRCQCLQTLQGIHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNSDKS  72
                                    10        20        30        40        50        60        70  

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with GROA_HUMAN | P09341 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:72
                                    44        54        64        74        84        94       104  
           GROA_HUMAN    35 ASVATELRCQCLQTLQGIHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNSDKS 106
               SCOP domains d1msgb_ B: Melanoma growth stimulating activity (MGSA)                   SCOP domains
               CATH domains 1msgB00 B:1-72  [code=2.40.50.40, no name defined]                       CATH domains
           Pfam domains (1) IL8-1msgB01 B:1-67                                                 ----- Pfam domains (1)
           Pfam domains (2) IL8-1msgB02 B:1-67                                                 ----- Pfam domains (2)
         Sec.struct. author ........................eeeee.........eeeee.....eee.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------SMALL_CYTOKINES_CXC  PDB: B:9-53             ------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:1-41 UniProt: 34-75     ---------------------------1.4  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3a  PDB: B:41-69      --- Transcript 1 (2)
                 1msg B   1 ASVATELRCQCLQTLQGIHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVKKIIEKMLNSDKS  72
                                    10        20        30        40        50        60        70  

   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)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A,B   (GROA_HUMAN | P09341)
molecular function
    GO:0045236    CXCR chemokine receptor binding    Interacting selectively and non-covalently with a chemokine receptor in the CXCR family.
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    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: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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 Visualization

(-) Interactive Views

NMR Structure
  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 1msg)
 
  Sites
(no "Sites" information available for 1msg)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1msg)
 

(-) 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
  1msg
    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
  GROA_HUMAN | P09341
    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
  GROA_HUMAN | P09341
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GROA_HUMAN | P093411mgs 1msh 1rod

(-) Related Entries Specified in the PDB File

1msh