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(-) Description

Title :  SOLUTION STRUCTURE OF THE MIT DOMAIN FROM HUMAN SPARTIN
 
Authors :  T. Suetake, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Apr 06  (Deposition) - 14 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Spartin, Spg20, Mit, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Suetake, F. Hayashi, S. Yokoyama
Solution Structure Of The Mit Domain From Human Spartin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPARTIN
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050725-19
    Expression System Vector TypePLASMID
    FragmentMIT DOMAIN
    GeneSPG20, KIAA0610, TAHCCP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymTRANS-ACTIVATED BY HEPATITIS C VIRUS CORE PROTEIN 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DL1)

(-) Sites  (0, 0)

(no "Site" information available for 2DL1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DL1)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003551821aENSE00001615620chr13:36944317-3694422692SPG20_HUMAN-00--
1.6fENST000003551826fENSE00002200797chr13:36909969-36909158812SPG20_HUMAN1-2702701A:1-116 (gaps)150
1.7ENST000003551827ENSE00000907425chr13:36905733-36905536198SPG20_HUMAN271-336660--
1.8aENST000003551828aENSE00000907424chr13:36903654-36903499156SPG20_HUMAN337-388520--
1.10aENST0000035518210aENSE00000907422chr13:36900835-36900712124SPG20_HUMAN389-430420--
1.12bENST0000035518212bENSE00000907420chr13:36888558-36888364195SPG20_HUMAN430-495660--
1.14bENST0000035518214bENSE00000907418chr13:36886614-36886456159SPG20_HUMAN495-548540--
1.15aENST0000035518215aENSE00000907416chr13:36886372-3688628291SPG20_HUMAN548-578310--
1.17eENST0000035518217eENSE00001400000chr13:36878769-368757772993SPG20_HUMAN578-666890--

(-) 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:116
 aligned with SPG20_HUMAN | Q8N0X7 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
          SPG20_HUMAN     2 EQEPQNGEPAEIKIIREAYKKAFLFVNKGLNTDELGQKEEAKNYYKQGIGHLLRGISISSKESEHTGPGWESARQMQQKMKETLQNVRTRLEILEKGLATSLQNDLQEVPKLYPEFPPKDMCEKLPEPQSFSSAPQHAEVNGNTSTPSAG 151
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........----------------------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.6f  PDB: A:1-116 (gaps) UniProt: 1-270 [INCOMPLETE]                                                                                             Transcript 1
                 2dl1 A   1 GSSGSSGEPAEIKIIREAYKKAFLFVNKGLNTDELGQKEEAKNYYKQGIGHLLRGISISSKESEHTGPGWESARQMQQKMKETLQNVRTRLEILEKGLATSLQNDLQEVP----------------------------------SGPSSG 116
                                    10        20        30        40        50        60        70        80        90       100       110         -         -         -    |  116
                                                                                                                                       110                                111     

   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 2DL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DL1)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (SPG20_HUMAN | Q8N0X7)
molecular function
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009838    abscission    The controlled shedding of a body part.
    GO:0060612    adipose tissue development    The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0034389    lipid particle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0048698    negative regulation of collateral sprouting in absence of injury    Any process that stops, prevents, or reduces the frequency, rate or extent of collateral sprouting in the absence of injury.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0051881    regulation of mitochondrial membrane potential    Any process that modulates the establishment or extent of the mitochondrial membrane potential, the electric potential existing across the mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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        SPG20_HUMAN | Q8N0X74u7i

(-) Related Entries Specified in the PDB File

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