Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF A PROLACTIN ANTAGONIST
 
Authors :  I. J. L. Broutin, A. Ducruix, J. B. Jomain, V. Goffin
Date :  12 Jun 07  (Deposition) - 11 Sep 07  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Antagonist Receptor Interaction, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Jomain, E. Tallet, I. Broutin, S. Hoos, J. Van Agthoven, A. Ducruix, P. A. Kelly, B. B. Kragelund, P. England, V. Goffin
Structural And Thermodynamic Bases For The Design Of Pure Prolactin Receptor Antagonists: X-Ray Structure Of Del1-9-G129R-Hprl.
J. Biol. Chem. V. 282 33118 2007
PubMed-ID: 17785459  |  Reference-DOI: 10.1074/JBC.M704364200

(-) Compounds

Molecule 1 - PROLACTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPQE70
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePRL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPRL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Q98)

(-) Sites  (0, 0)

(no "Site" information available for 2Q98)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:58 -A:174

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q98)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOMATOTROPIN_1PS00266 Somatotropin, prolactin and related hormones signature 1.PRL_HUMAN86-119  1A:58-91
2SOMATOTROPIN_2PS00338 Somatotropin, prolactin and related hormones signature 2.PRL_HUMAN202-219  1A:174-191

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003064821ENSE00001148399chr6:22297730-22297184547PRL_HUMAN1-10100--
1.2cENST000003064822cENSE00001174381chr6:22294813-22294638176PRL_HUMAN10-68591A:9-4032
1.3ENST000003064823ENSE00001174368chr6:22292874-22292767108PRL_HUMAN69-104361A:41-7636
1.4ENST000003064824ENSE00001174359chr6:22290582-22290403180PRL_HUMAN105-164601A:77-13660
1.5ENST000003064825ENSE00001148390chr6:22287822-22287480343PRL_HUMAN165-227631A:137-19963

(-) Sequences/Alignments

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:191
 aligned with PRL_HUMAN | P01236 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:191
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226 
            PRL_HUMAN    37 ARCQVTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYTHGRGFITKAINSCHTSSLATPEDKEQAQQMNQKDFLSLIVSILRSWNEPLYHLVTEVRGMQEAPEAILSKAVEIEEQTKRLLEGMELIVSQVHPETKENEIYPVWSGLPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCRIIHNNNC 227
               SCOP domains d2q98a_ A: Prolactin (placental lactogen)                                                                                                                                                       SCOP domains
               CATH domains 2q98A00 A:9-199  [code=1.20.1250.10, no name defined]                                                                                                                                           CATH domains
               Pfam domains ---Hormone_1-2q98A01 A:12-199                                                                                                                                                                   Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------SOMATOTROPIN_1  PDB: A:58-91      ----------------------------------------------------------------------------------SOMATOTROPIN_2    -------- PROSITE
               Transcript 1 Exon 1.2c  PDB: A:9-40          Exon 1.3  PDB: A:41-76              Exon 1.4  PDB: A:77-136 UniProt: 105-164                    Exon 1.5  PDB: A:137-199 UniProt: 165-227                       Transcript 1
                 2q98 A   9 MRSQVTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYTHGRGFITKAINSCHTSSLATPEDKEQAQQMNQKDFLSLIVSILRSWNEPLYHLVTEVRGMQEAPEAILSKAVEIEEQTKRLLERMELIVSQVHPETKENEIYPVWSGLPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCRIIHNNNC 199
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRL_HUMAN | P01236)
molecular function
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    GO:0005148    prolactin receptor binding    Interacting selectively and non-covalently with the prolactin receptor.
    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).
biological process
    GO:0060397    JAK-STAT cascade involved in growth hormone signaling pathway    The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0046427    positive regulation of JAK-STAT cascade    Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
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: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

Asymmetric/Biological 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 2q98)
 
  Sites
(no "Sites" information available for 2q98)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2q98)
 

(-) 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
  2q98
    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
  PRL_HUMAN | P01236
    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
  PRL_HUMAN | P01236
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRL_HUMAN | P012361rw5 3d48 3ew3 3mzg 3n06 3n0p 3ncb 3ncc 3nce 3ncf 3npz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q98)