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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL BARPEPTIDE IN DPC MICELLES
 
Authors :  C. Loew, U. Weininger, J. Balbach
Date :  16 Dec 07  (Deposition) - 14 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Barpeptide, Micelle, Nmr-Structure, Alternative Splicing, Anti-Oncogene, Cell Cycle, Coiled Coil, Cytoplasm, Developmental Protein, Differentiation, Disease Mutation, Endocytosis, Host-Virus Interaction, Nucleus, Phosphoprotein, Sh3 Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Low, U. Weininger, H. Lee, K. Schweimer, I. Neundorf, A. G. Beck-Sickinger, R. W. Pastor, J. Balbach
Structure And Dynamics Of Helix-0 Of The N-Bar Domain In Lipid Micelles And Bilayers
Biophys. J. V. 95 4315 2008
PubMed-ID: 18658220  |  Reference-DOI: 10.1529/BIOPHYSJ.108.134155
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYC BOX-DEPENDENT-INTERACTING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainK12
    Expression System Taxid562
    Expression System VariantBL21
    Expression System VectorPETSUMO
    Expression System Vector TypeVECTOR
    FragmentBARPEPTIDE, UNP RESIDUES 1-33
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRIDGING INTEGRATOR 1, AMPHIPHYSIN-LIKE PROTEIN, AMPHIPHYSIN II, BOX-DEPENDENT MYC- INTERACTING PROTEIN 1

 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 2RND)

(-) Sites  (0, 0)

(no "Site" information available for 2RND)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BARPS51021 BAR domain profile.BIN1_HUMAN29-276  1A:29-34

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003167241aENSE00001918151chr2:127864931-127864436496BIN1_HUMAN1-28281A:1-2828
1.2ENST000003167242ENSE00000925832chr2:127834282-12783420281BIN1_HUMAN29-55271A:29-335
1.3ENST000003167243ENSE00000925829chr2:127828392-12782833855BIN1_HUMAN56-74190--
1.4ENST000003167244ENSE00000925827chr2:127828223-12782812995BIN1_HUMAN74-105320--
1.5ENST000003167245ENSE00000925826chr2:127827666-12782757196BIN1_HUMAN106-137320--
1.6ENST000003167246ENSE00000925823chr2:127826607-127826500108BIN1_HUMAN138-173360--
1.7ENST000003167247ENSE00000925822chr2:127825831-12782573993BIN1_HUMAN174-204310--
1.9ENST000003167249ENSE00000925821chr2:127821594-12782150986BIN1_HUMAN205-233290--
1.10ENST0000031672410ENSE00000925819chr2:127821222-12782114776BIN1_HUMAN233-258260--
1.11ENST0000031672411ENSE00000925816chr2:127819773-12781969183BIN1_HUMAN259-286280--
1.13ENST0000031672413ENSE00000925814chr2:127816731-127816587145BIN1_HUMAN286-334490--
1.14ENST0000031672414ENSE00000925812chr2:127815177-127815049129BIN1_HUMAN335-377430--
1.15bENST0000031672415bENSE00000925811chr2:127811588-127811481108BIN1_HUMAN378-413360--
1.15cENST0000031672415cENSE00001417047chr2:127811021-12781099824BIN1_HUMAN414-42180--
1.15dENST0000031672415dENSE00001236385chr2:127809938-127809831108BIN1_HUMAN422-457360--
1.16ENST0000031672416ENSE00000964173chr2:127808819-12780873090BIN1_HUMAN458-487300--
1.17ENST0000031672417ENSE00000925804chr2:127808488-127808378111BIN1_HUMAN488-524370--
1.18aENST0000031672418aENSE00000925801chr2:127808098-127807997102BIN1_HUMAN525-558340--
1.19cENST0000031672419cENSE00001928062chr2:127806209-127805603607BIN1_HUMAN559-593350--

(-) 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:34
 aligned with BIN1_HUMAN | O00499 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:68
                                    10        20        30        40        50        60        
            BIN1_HUMAN    1 MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTY 68
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -----------------BAR-2rndA01     ----------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh----------------------------------h Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------BAR  PDB: A:29-34 UniProt: 29-276        PROSITE
               Transcript 1 Exon 1.1a  PDB: A:1-28      Exon 1.2  PDB: A:29-33     Exon 1.3      Transcript 1
                  2rnd A  1 MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKL----------------------------------Y 34
                                    10        20        30  |      -         -         -       |
                                                           33                                 34

   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 2RND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (BIN1_HUMAN | O00499)
molecular function
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0048156    tau protein binding    Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0060988    lipid tube assembly    The aggregation, arrangement and bonding together of a set of macromolecules to form a macromolecular complex that contains a tube of lipid surrounded by a protein coat involved in membrane shaping of vesicle membranes as they fuse or undergo fission.
    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:0042692    muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
    GO:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    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:0048711    positive regulation of astrocyte differentiation    Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
    GO:0071156    regulation of cell cycle arrest    Any process that modulates the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0030315    T-tubule    Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043194    axon initial segment    Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0060987    lipid tube    A macromolecular complex that contains a tube of lipid surrounded by a protein coat.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0033268    node of Ranvier    An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed.
    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.

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

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        BIN1_HUMAN | O004991muz 1mv0 1mv3 2fic 2rmy 5i22

(-) Related Entries Specified in the PDB File

2rmy