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(-) Description

Title :  BRAIN TUMOR NHL DOMAIN
 
Authors :  T. A. Edwards, B. D. Wilkinson, R. P. Wharton, A. K. Aggarwal
Date :  18 Aug 03  (Deposition) - 21 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Brat, Nhl Domain, Nhl Repeat, Beta-Propeller, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Edwards, B. D. Wilkinson, R. P. Wharton, A. K. Aggarwal
Model Of The Brain Tumor-Pumilio Translation Repressor Complex
Genes Dev. V. 17 2508 2003
PubMed-ID: 14561773  |  Reference-DOI: 10.1101/GAD.1119403
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BRAIN TUMOR CG10719-PA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET19B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentBRAIN TUMOR NHL DOMAIN
    GeneBRAIN TUMOR
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymNHL

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q7F)

(-) Sites  (0, 0)

(no "Site" information available for 1Q7F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q7F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q7F)

(-) PROSITE Motifs  (1, 10)

Asymmetric Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NHLPS51125 NHL repeat profile.BRAT_DROME767-810
 
814-859
 
860-901
 
902-944
 
945-988
 
  10A:767-810
B:767-810
A:814-859
B:814-859
A:860-901
B:860-901
A:902-944
B:902-944
A:945-988
B:945-988
Biological Unit 1 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NHLPS51125 NHL repeat profile.BRAT_DROME767-810
 
814-859
 
860-901
 
902-944
 
945-988
 
  5A:767-810
-
A:814-859
-
A:860-901
-
A:902-944
-
A:945-988
-
Biological Unit 2 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NHLPS51125 NHL repeat profile.BRAT_DROME767-810
 
814-859
 
860-901
 
902-944
 
945-988
 
  5-
B:767-810
-
B:814-859
-
B:860-901
-
B:902-944
-
B:945-988

(-) Exons   (0, 0)

(no "Exon" information available for 1Q7F)

(-) 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:279
 aligned with BRAT_DROME | Q8MQJ9 from UniProtKB/Swiss-Prot  Length:1037

    Alignment length:279
                                   768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028         
          BRAT_DROME    759 IKRQKMIYHCKFGEFGVMEGQFTEPSGVAVNAQNDIIVADTNNHRIQIFDKEGRFKFQFGECGKRDSQLLYPNRVAVVRNSGDIIVTERSPTHQIQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVECKVMRVIIFDQNGNVLHKFGCSKHLEFPNGVVVNDKQEIFISDNRAHCVKVFNYEGQYLRQIGGEGITNYPIGVGINSNGEILIADNHNNFNLTIFTQDGQLISALESKVKHAQCFDVALMDDGSVVLASKDYRLYIYRYVQLAPVGM 1037
               SCOP domains d1q7fa_ A: Brain tumor cg10719-pa                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1q7fA00 A:759-1037 TolB, C-terminal domain                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.eeeee................ee.....eeeeehhhheeeee.....eeeee............eeeeee......eeeee.hhhheeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeeee.......eeeeee....eeeeee.hhheeeeee....eeeee........eeeeee.....eeeee.....eeeee.....eeeeeee......eeeeeee...eeeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------NHL  PDB: A:767-810 UniProt: 767-810        ---NHL  PDB: A:814-859 UniProt: 814-859          NHL  PDB: A:860-901 UniProt: 860-901      NHL  PDB: A:902-944 UniProt: 902-944       NHL  PDB: A:945-988 UniProt: 945-988        ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q7f A  759 IKRQRMIYHCKFGEFGVMEGQFTEPSGVAVNAQNDIIVADTNNHRIQIFDKEGRFKFQFGECGKRDSQLLYPNRVAVVRNSGDIIVTERSPTHQIQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVECKVMRVIIFDQNGNVLHKFGCSKHLEFPNGVVVNDKQEIFISDNRAHCVKVFNYEGQYLRQIGGEGITNYPIGVGINSNGEILIADNHNNFNLTIFTQDGQLISALESKVKHAQCFDVALMDDGSVVLASKDYRLYIYRYVQLAPVGM 1037
                                   768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028         

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with BRAT_DROME | Q8MQJ9 from UniProtKB/Swiss-Prot  Length:1037

    Alignment length:282
                                   765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035  
          BRAT_DROME    756 KSQIKRQKMIYHCKFGEFGVMEGQFTEPSGVAVNAQNDIIVADTNNHRIQIFDKEGRFKFQFGECGKRDSQLLYPNRVAVVRNSGDIIVTERSPTHQIQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVECKVMRVIIFDQNGNVLHKFGCSKHLEFPNGVVVNDKQEIFISDNRAHCVKVFNYEGQYLRQIGGEGITNYPIGVGINSNGEILIADNHNNFNLTIFTQDGQLISALESKVKHAQCFDVALMDDGSVVLASKDYRLYIYRYVQLAPVGM 1037
               SCOP domains d1q7fb_ B: Brain tumor cg10719-pa                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1q7fB00 B:756-1037 TolB, C-terminal domain                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB01 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB02 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB03 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB04 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB05 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------NHL-1q7fB06 B:914-941       ------------------------------------------------------------------------------------------------ Pfam domains (6)
         Sec.struct. author ......eee.eeeee............eeeeee.....eeeee.hhheeeee.....eeeee............eeeeee......eeeee.hhhheeeee.....eeeee.......eeeeee.....eeeee....eeeee.....eeeeee.......eeeeee....eeeeee....eeeeee....eeeee........eeeeee.....eeeee.....eeeee.....eeeeeee......eeeeee....eeeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------NHL  PDB: B:767-810 UniProt: 767-810        ---NHL  PDB: B:814-859 UniProt: 814-859          NHL  PDB: B:860-901 UniProt: 860-901      NHL  PDB: B:902-944 UniProt: 902-944       NHL  PDB: B:945-988 UniProt: 945-988        ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q7f B  756 KSQIKRQRMIYHCKFGEFGVMEGQFTEPSGVAVNAQNDIIVADTNNHRIQIFDKEGRFKFQFGECGKRDSQLLYPNRVAVVRNSGDIIVTERSPTHQIQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVECKVMRVIIFDQNGNVLHKFGCSKHLEFPNGVVVNDKQEIFISDNRAHCVKVFNYEGQYLRQIGGEGITNYPIGVGINSNGEILIADNHNNFNLTIFTQDGQLISALESKVKHAQCFDVALMDDGSVVLASKDYRLYIYRYVQLAPVGM 1037
                                   765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035  

   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)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Family: NHL (2)
1aNHL-1q7fB01B:914-941
1bNHL-1q7fB02B:914-941
1cNHL-1q7fB03B:914-941
1dNHL-1q7fB04B:914-941
1eNHL-1q7fB05B:914-941
1fNHL-1q7fB06B:914-941

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BRAT_DROME | Q8MQJ9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0045182    translation regulator activity    Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
    GO:0030371    translation repressor activity    Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008356    asymmetric cell division    The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.
    GO:0055060    asymmetric neuroblast division resulting in ganglion mother cell formation    Any process resulting in the physical partitioning and separation of a neuroblast into a neuroblast and a ganglion mother cell.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    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:0007402    ganglion mother cell fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a ganglion mother cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0007406    negative regulation of neuroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0007400    neuroblast fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
    GO:0007405    neuroblast proliferation    The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron.
    GO:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0008582    regulation of synaptic growth at neuromuscular junction    Any process that modulates the frequency, rate or extent of synaptic growth at neuromuscular junctions.
    GO:1900242    regulation of synaptic vesicle endocytosis    Any process that modulates the frequency, rate or extent of synaptic vesicle endocytosis.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0035282    segmentation    The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis.
    GO:0007419    ventral cord development    The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms.
cellular component
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    GO:0045180    basal cortex    The region that lies just beneath the plasma membrane on the basal edge of a cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRAT_DROME | Q8MQJ94zlr 5ex7

(-) Related Entries Specified in the PDB File

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