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(-) Description

Title :  NEW PROTEIN FOLD REVEALED BY A 2.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NERVE GROWTH FACTOR
 
Authors :  N. Q. Mcdonald, R. Lapatto, J. Murray-Rust, J. Gunning, A. Wlodawer, T. L. Blundell
Date :  08 Apr 93  (Deposition) - 31 May 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Q. Mcdonald, R. Lapatto, J. Murray-Rust, J. Gunning, A. Wlodawer, T. L. Blundell
New Protein Fold Revealed By A 2. 3-A Resolution Crystal Structure Of Nerve Growth Factor.
Nature V. 354 411 1991
PubMed-ID: 1956407  |  Reference-DOI: 10.1038/354411A0

(-) Compounds

Molecule 1 - BETA-NERVE GROWTH FACTOR
    ChainsA
    EngineeredYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BET)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:15 -A:80
2A:58 -A:108
3A:68 -A:110

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NGF_1PS00248 Nerve growth factor family signature.NGF_MOUSE188-201  1A:67-80
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NGF_1PS00248 Nerve growth factor family signature.NGF_MOUSE188-201  2A:67-80

(-) Exons   (0, 0)

(no "Exon" information available for 1BET)

(-) 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:107
 aligned with NGF_MOUSE | P01139 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:107
                                   140       150       160       170       180       190       200       210       220       230       
            NGF_MOUSE   131 GEFSVCDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSKHWNSYCTTTHTFVKALTTDEKQAAWRFIRIDTACVCVLSRKA 237
               SCOP domains d1beta_ A: beta-Nerve growth factor                                                                         SCOP domains
               CATH domains 1betA00 A:10-116 Cystine-knot cytokines                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeee....eeeee..............eeeeeee.................eeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------NGF_1         ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bet A  10 GEFSVCDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSKHWNSYCTTTHTFVKALTTDEKQAAWRFIRIDTACVCVLSRKA 116
                                    19        29        39        49        59        69        79        89        99       109       

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BET)

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)
Chain A   (NGF_MOUSE | P01139)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces 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:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0005163    nerve growth factor receptor binding    Interacting selectively and non-covalently with the nerve growth factor receptor.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
    GO:0030297    transmembrane receptor protein tyrosine kinase activator activity    Binds to and increases the activity of a transmembrane receptor protein tyrosine kinase.
biological process
    GO:0007171    activation of transmembrane receptor protein tyrosine kinase activity    Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0008625    extrinsic apoptotic signaling pathway via death domain receptors    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0032455    nerve growth factor processing    The generation of a mature nerve growth factor (NGF) by proteolysis of a precursor.
    GO:0038180    nerve growth factor signaling pathway    A series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0007422    peripheral nervous system development    The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045773    positive regulation of axon extension    Any process that activates or increases the frequency, rate or extent of axon extension.
    GO:0048672    positive regulation of collateral sprouting    Any process that activates or increases the frequency, rate or extent of collateral sprouting.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0014042    positive regulation of neuron maturation    Any process that activates or increases the frequency, rate or extent of neuron maturation.
    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:0051388    positive regulation of neurotrophin TRK receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of the neurotrophin TRK receptor signaling pathway.
    GO:0031954    positive regulation of protein autophosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation by a protein of one or more of its own residues.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    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:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
    GO:0046928    regulation of neurotransmitter secretion    Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell.
    GO:0051279    regulation of release of sequestered calcium ion into cytosol    Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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.

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        NGF_MOUSE | P011391btg 1sgf 3ij2 4eax 4xpj 5lsd

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