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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN REDD1, A HYPOXIA-INDUCED REGULATOR OF MTOR
 
Authors :  S. Vega-Rubin-De-Celis, Z. Abdallah, J. Brugarolas, X. Zhang
Date :  08 Feb 10  (Deposition) - 09 Mar 10  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Redd1 Ddit4 Mtor, Hypoxia, Cancer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Vega-Rubin-De-Celis, Z. Abdallah, L. Kinch, N. V. Grishin, J. Brugarolas, X. Zhang
Structural Analysis And Functional Implications Of The Negative Mtorc1 Regulator Redd1.
Biochemistry V. 49 2491 2010
PubMed-ID: 20166753  |  Reference-DOI: 10.1021/BI902135E

(-) Compounds

Molecule 1 - DNA-DAMAGE-INDUCIBLE TRANSCRIPT 4 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET28 WITH A HIS6-SUMO TAG
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FUNCTIONAL DOMAIN
    GeneDDIT4, REDD1, RTP801
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN REGULATED IN DEVELOPMENT AND DNA DAMAGE RESPONSE 1, REDD-1, HIF-1 RESPONSIVE PROTEIN RTP801

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LQ9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LQ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LQ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3LQ9)

(-) 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:128
 aligned with DDIT4_HUMAN | Q9NX09 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:134
                                    98       108       118       128       138       148       158       168       178       188       198       208       218    
          DDIT4_HUMAN    89 DEHLCANLMQLLQESLAQARLGSRRPARLLMPSQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLRLDSRLWPKIQGLFSSANSPFLPGFSQSLTLSTGFRVIKKKLY 222
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.ee.....ee.ee.hhhhhhhhhhhhhhhhh...hhhh.eeeeeeeee..eeeeeeeee........eeeeeeee......-............-----.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lq9 A  89 DEHLCANLmQLLQESLAQARLGSRRPARLLmPSQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLRLDSRLW-KIQGLFSSANSP-----SQSLTLSTGFRVIKKKLY 222
                                    98       108       118|      128       138       148       158       168       178       188       198|     |208       218    
                                   97-MSE               119-MSE                                                            186 |        199   205                 
                                                                                                                             188                                  

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with DDIT4_HUMAN | Q9NX09 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:135
                                    97       107       117       127       137       147       157       167       177       187       197       207       217     
          DDIT4_HUMAN    88 EDEHLCANLMQLLQESLAQARLGSRRPARLLMPSQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLRLDSRLWPKIQGLFSSANSPFLPGFSQSLTLSTGFRVIKKKLY 222
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------RTP801_C-3lq9B01 B:104-222                                                                                              Pfam domains (1)
           Pfam domains (2) ----------------RTP801_C-3lq9B02 B:104-222                                                                                              Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh.ee.....ee.ee.hhhhhhhhhhhhhhhhh...hhhh.eeeeeeeee..eeeeeeeee........eeeeeeee.......-.......---.-----.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lq9 B  88 SDEHLCANLmQLLQESLAQARLGSRRPARLLmPSQLVSQVGKELLRLAYSEPCGLRGALLDVCVEQGKSCHSVGQLALDPSLVPTFQLTLVLRLDSRLWP-IQGLFSS---P-----SQSLTLSTGFRVIKKKLY 222
                                    97       107       117 |     127       137       147       157       167       177       187 |     | - |     207       217     
                                    97-MSE               119-MSE                                                             187 |   195 199   205                 
                                                                                                                               189                                 

   Legend:   → Mismatch (orange background)
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    → 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 3LQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQ9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDIT4_HUMAN | Q9NX09)
molecular function
    GO:0071889    14-3-3 protein binding    Interacting selectively and non-covalently with a 14-3-3 protein. A 14-3-3 protein is any of a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells, and have been implicated in the modulation of distinct biological processes by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins.
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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0042771    intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0032007    negative regulation of TOR signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
    GO:0045820    negative regulation of glycolytic process    Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
    GO:1902532    negative regulation of intracellular signal transduction    Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0010801    negative regulation of peptidyl-threonine phosphorylation    Any process that decreases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0048011    neurotrophin TRK receptor signaling pathway    A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:1901216    positive regulation of neuron death    Any process that activates or increases the frequency, rate or extent of neuron death.
    GO:0043241    protein complex disassembly    The disaggregation of a protein complex into its constituent components. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0001666    response to hypoxia    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 a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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