Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  DNUMB PTB DOMAIN COMPLEXED WITH A PHOSPHOTYROSINE PEPTIDE, NMR, ENSEMBLE OF STRUCTURES.
 
Authors :  S. -C. Li, C. Zwahlen, S. J. F. Vincent, C. J. Mcglade, T. Pawson, J. D. Forman-Kay
Date :  29 Oct 98  (Deposition) - 04 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (14x)
Keywords :  Complex, Signal Transduction, Phosphotyrosine Binding Domain (Ptb), Asymetr Ic Cell Division, Cell Cycle/Gene Regulation Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Li, C. Zwahlen, S. J. Vincent, C. J. Mcglade, L. E. Kay, T. Pawson, J. D. Forman-Kay
Structure Of A Numb Ptb Domain-Peptide Complex Suggests A Basis For Diverse Binding Specificity.
Nat. Struct. Biol. V. 5 1075 1998
PubMed-ID: 9846878  |  Reference-DOI: 10.1038/4185
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NUMB PROTEIN)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX4T2
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    FragmentPTB DOMAIN
    GeneNUMB
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - PROTEIN (GPPY PEPTIDE)
    ChainsB
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (14x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 2NMB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NMB)

(-) Cis Peptide Bonds  (1, 2)

NMR Structure
No.ModelResidues
18, 12Gly B:4 -Pro B:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.NUMB_DROME81-208  1A:81-205

(-) Exons   (0, 0)

(no "Exon" information available for 2NMB)

(-) 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:147
 aligned with NUMB_DROME | P16554 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:164
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
           NUMB_DROME    64 SKPHQWQADEEAVRSATCSFSVKYLGCVEVFESRGMQVCEEALKVLRQSRRRPVRGLLHVSGDGLRVVDDETKGLIVDQTIEKVSFCAPDRNHERGFSYICRDGTTRRWMCHGFLACKDSGERLSHAVGCAFAVCLERKQRRDKECGVTMTFDTKNSTFTRTGS 227
               SCOP domains d2nmba_ A: Numb                                                                                                                                                      SCOP domains
               CATH domains 2nmbA00 A:64-210 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                                                                         CATH domains
               Pfam domains -------------------PID-2nmbA01 A:83-205                                                                                                       ---------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhh......eeee......eeee..............................eee......eeeeeeee.......hhhhhhhhh..........-----------------..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PID  PDB: A:81-205 UniProt: 81-208                                                                                              ------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nmb A  64 SKPHQWQADEEAVRSATCSFSVKYLGCVEVFESRGMQVCEEALKVLRQSRRRPVRGLLHVSGDGLRVVDDETKGLIVDQTIEKVSFCAPDRNHERGFSYICRDGTTRRWMCHGFLACKDSGERLSHAVGCAFAVCLERKQRR-----------------TRAAA 210
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203 |       -       206    
                                                                                                                                                                       205               206    

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2nmb B   1 AYIGPyL   7
                                 | 
                                 6-PTR

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PH (111)

(-) Gene Ontology  (38, 38)

NMR Structure(hide GO term definitions)
Chain A   (NUMB_DROME | P16554)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0061382    Malpighian tubule tip cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a Malpighian tubule tip cell. A Malpighian tubule tip cell is a mitogenic signaling cell that controls the proliferation of its neighboring cells.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0055059    asymmetric neuroblast division    The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0051642    centrosome localization    Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
    GO:0035050    embryonic heart tube development    The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
    GO:0008347    glial cell migration    The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0042694    muscle cell fate specification    The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
    GO:0045746    negative regulation of Notch signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
    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:0061320    pericardial nephrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is an insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    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:0045807    positive regulation of endocytosis    Any process that activates or increases the frequency, rate or extent of endocytosis.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0008593    regulation of Notch signaling pathway    Any process that modulates the frequency, rate or extent of the Notch signaling pathway.
    GO:0009786    regulation of asymmetric cell division    Any process that modulates the frequency, rate or extent of asymmetric cell division.
    GO:0051960    regulation of nervous system development    Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0007622    rhythmic behavior    The specific behavior of an organism that recur with measured regularity.
    GO:0045035    sensory organ precursor cell division    The series of four asymmetric divisions undergone by the sensory organ precursor cells to generate cells that have distinct cell fates. For example, in the external sensory organ, the precursor cells give rise to one multidendritic neuron and four additional cells (the socket, shaft, sheath cells and the external sense neuron).
    GO:0016360    sensory organ precursor cell fate determination    The process in which a cell becomes capable of differentiating autonomously into a sensory organ precursor cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    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:0045180    basal cortex    The region that lies just beneath the plasma membrane on the basal edge of a cell.
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

NMR Structure
  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
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2nmb)
 
  Cis Peptide Bonds
    Gly B:4 - Pro B:5   [ RasMol ]  
 

(-) 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
  2nmb
    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
  NUMB_DROME | P16554
    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
  NUMB_DROME | P16554
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NUMB_DROME | P165541ddm

(-) Related Entries Specified in the PDB File

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