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(-) Description

Title :  HUMAN GRANULIN A
 
Authors :  D. Tolkatchev, P. Wang, Z. Chen, P. Xu, F. Ni
Date :  13 Dec 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Granulin A, Epithelin, Human, Stack Of Hairpins, Alternative Splicing, Cytokine, Glycoprotein, Polymorphism, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Tolkatchev, S. Malik, A. Vinogradova, P. Wang, Z. Chen, P. Xu, H. P. Bennett, A. Bateman, F. Ni
Structure Dissection Of Human Progranulin Identifies Well-Folded Granulin/Epithelin Modules With Unique Functional Activities.
Protein Sci. V. 17 711 2008
PubMed-ID: 18359860  |  Reference-DOI: 10.1110/PS.073295308
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GRANULIN A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainORIGAMI(DE3)
    Expression System Taxid562
    Expression System VectorPET-32
    GeneGRN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2JYE)

(-) SS Bonds  (6, 6)

NMR Structure
No.Residues
1A:6 -A:18
2A:12 -A:28
3A:19 -A:36
4A:29 -A:43
5A:37 -A:50
6A:44 -A:57

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064634S398LGRN_HUMANPolymorphism148213321AH68L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRANULINSPS00799 Granulins signature.GRN_HUMAN92-105
158-171
240-253
315-328
397-410
475-488
552-565
  2-
-
-
A:37-50
A:70-72
-
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000538671aENSE00001349955chr17:42422491-42422702212GRN_HUMAN-00--
1.2ENST000000538672ENSE00002158819chr17:42426526-42426670145GRN_HUMAN1-46460--
1.3ENST000000538673ENSE00001719716chr17:42426794-42426919126GRN_HUMAN47-88420--
1.4ENST000000538674ENSE00001703280chr17:42427035-4242711985GRN_HUMAN89-117290--
1.5ENST000000538675ENSE00001749873chr17:42427596-42427708113GRN_HUMAN117-154380--
1.6bENST000000538676bENSE00000732204chr17:42427810-42427945136GRN_HUMAN155-200460--
1.7ENST000000538677ENSE00000732203chr17:42428059-42428168110GRN_HUMAN200-236370--
1.8aENST000000538678aENSE00001255741chr17:42428405-42428531127GRN_HUMAN237-279431A:1-11
1.9ENST000000538679ENSE00000732201chr17:42428731-4242882898GRN_HUMAN279-311331A:1-3333
1.10bENST0000005386710bENSE00000854270chr17:42428918-42429163246GRN_HUMAN312-393821A:34-67 (gaps)40
1.11ENST0000005386711ENSE00000732199chr17:42429383-42429616234GRN_HUMAN394-471781A:68-725
1.12aENST0000005386712aENSE00000732197chr17:42429709-42429939231GRN_HUMAN472-548770--
1.13ENST0000005386713ENSE00001376066chr17:42430029-42430470442GRN_HUMAN549-593450--

(-) 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 GRN_HUMAN | P28799 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:124
                                   288       298       308       318       328       338       348       358       368       378       388       398    
            GRN_HUMAN   279 VGDVKCDMEVSCPDGYTCCRLQSGAWGCCPFTQAVCCEDHIHCCPAGFTCDTQKGTCEQGPHQVPWMEKAPAHLSLPDPQALKRDVPCDNVSSCPSSDTCCQLTSGEWGCCPIPEAVCCSDHQH 402
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------Granulin-2jyeA01 A:17-59                   ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee.....eeeee...................ee....ee...------.......----------------------------------------------..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------L---- SAPs(SNPs)
                    PROSITE ------------------------------------GRANULINS     --------------------------------------------------------------------GRANUL PROSITE
           Transcript 1 (1) 1--------------------------------Exon 1.10b  PDB: A:34-67 (gaps) UniProt: 312-393 [INCOMPLETE]                     Exon 1.11 Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:1-33            ------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2jye A   1 AMDVKCDMEVSCPDGYTCCRLQSGAWGCCPFTQAVCCEDHIHCCPAGFTCDTQKGTCEQK------LAAALEH----------------------------------------------HHHHH  72
                                    10        20        30        40        50        60      | 64  |      -         -         -         -        68    
                                                                                      60     61    67                                             68    

   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 2JYE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (GRN_HUMAN | P28799)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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: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:0035988    chondrocyte proliferation    The multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0060179    male mating behavior    The specific behavior of a male organism that is associated with reproduction.
    GO:0061351    neural precursor cell proliferation    The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell.
    GO:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    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.
    GO:0048488    synaptic vesicle endocytosis    Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRN_HUMAN | P287991g26 2jyt 2jyu 2jyv

(-) Related Entries Specified in the PDB File

1fwo ORYZAIN BETA FRAGMENT
1g26 HUMAN GRANULIN A FRAGMENT
1qgm CARP GRANULIN-1 FRAGMENT