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(-) Description

Title :  STRUCTURE OF HUMAN MUNC18-2
 
Authors :  Y. Hackmann, S. C. Graham, S. Ehl, S. Hoening, K. Lehmberg, M. Arico, D. J G. G. Griffiths
Date :  21 Oct 13  (Deposition) - 30 Oct 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Hackmann, S. C. Graham, S. Ehl, S. Hoening, K. Lehmberg, M. Arico, D. J. Owen, G. G. Griffiths
Syntaxin Binding Mechanism And Disease-Causing Mutations In Munc18-2
Proc. Natl. Acad. Sci. Usa V. 110 E4482 2013
PubMed-ID: 24194549  |  Reference-DOI: 10.1073/PNAS.1313474110

(-) Compounds

Molecule 1 - SYNTAXIN-BINDING PROTEIN 2
    CellCYTOTOXIC T LYMPHOCYTES
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASBAC 1
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN UNC-18 HOMOLOG 2, UNC18-2, PROTEIN UNC-18 HOMOLOG B, UNC-18B, MUNC18-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:493 , PHE A:498BINDING SITE FOR RESIDUE CL A1594

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CCA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CCA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063814L209PSTXB2_HUMANDisease (FHL5)121918541AL209P
2UniProtVAR_063816R292HSTXB2_HUMANDisease (FHL5)746897867AR292H
3UniProtVAR_063817R405QSTXB2_HUMANDisease (FHL5)773360200AR405Q
4UniProtVAR_063818R405WSTXB2_HUMANDisease (FHL5)769717341AR405W
5UniProtVAR_063819P477LSTXB2_HUMANDisease (FHL5)121918540AP477L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CCA)

(-) Exons   (0, 0)

(no "Exon" information available for 4CCA)

(-) Sequences/Alignments

Asymmetric/Biological 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:542
 aligned with STXB2_HUMAN | Q15833 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:589
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584         
          STXB2_HUMAN     5 GLKAVVGEKILSGVIRSVKKDGEWKVLIMDHPSMRILSSCCKMSDILAEGITIVEDINKRREPIPSLEAIYLLSPTEKSVQALIKDFQGTPTFTYKAAHIFFTDTCPEPLFSELGRSRLAKVVKTLKEIHLAFLPYEAQVFSLDAPHSTYNLYCPFRAEERTRQLEVLAQQIATLCATLQEYPAIRYRKGPEDTAQLAHAVLAKLNAFKADTPSLGEGPEKTRSQLLIMDRAADPVSPLLHELTFQAMAYDLLDIEQDTYRYETTGLSEAREKAVLLDEDDDLWVELRHMHIADVSKKVTELLRTFCESKRLTTDKANIKDLSQILKKMPQYQKELNKYSTHLHLADDCMKHFKGSVEKLCSVEQDLAMGSDAEGEKIKDSMKLIVPVLLDAAVPAYDKIRVLLLYILLRNGVSEENLAKLIQHANVQAHSSLIRNLEQLGGTVTNPGGSGTSSRLEPRERMEPTYQLSRWTPVIKDVMEDAVEDRLDRNLWPFVSDPAPTASSQAAVSARFGHWHKNKAGIEARAGPRLIVYVMGGVAMSEMRAAYEVTRATEGKWEVLIGSSHILTPTRFLDDLKALDKKLEDIALP 593
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh............eeeeehhhhhhhhhh..hhhhhhh..eeee.............eeeeee..hhhhhhhhhhh..----.....eeeee....hhhhhhhhhh.hhhh.eeeeee.....ee....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhh.......hhhh.eeeeehhhhh.hhhhh...hhhhhhhhhh.....eeeee..-----.eeeee....hhhhhhhh.....hhhhhhhhhhhhhhhhhh---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh......------....................hhhhhhhhhhhh.................-----------------------....eeeeee....hhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.......... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------Q-----------------------------------------------------------------------L-------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cca A   5 GLKAVVGEKILSGVIRSVKKDGEWKVLIMDHPSMRILSSCCKMSDILAEGITIVEDINKRREPIPSLEAIYLLSPTEKSVQALIKDFQ----FTYKAAHIFFTDTCPEPLFSELGRSRLAKVVKTLKEIHLAFLPYEAQVFSLDAPHSTYNLYCPFRAEERTRQLEVLAQQIATLCATLQEYPAIRYRKGPEDTAQLAHAVLAKLNAFKADTPSLGEGPEKTRSQLLIMDRAADPVSPLLHELTFQAMAYDLLDIEQDTYRYETT-----REKAVLLDEDDDLWVELRHMHIADVSKKVTELLRTFCESKR---------DLSQILKKMPQYQKELNKYSTHLHLADDCMKHFKGSVEKLCSVEQDLAMGSDAEGEKIKDSMKLIVPVLLDAAVPAYDKIRVLLLYILLRNGVSEENLAKLIQHANVQAHSSLIRNLEQLGGTVTN------SSRLEPRERMEPTYQLSRWTPVIKDVMEDAVEDRLDRNLWPFVSDPAPT-----------------------RAGPRLIVYVMGGVAMSEMRAAYEVTRATEGKWEVLIGSSHILTPTRFLDDLKALDKKLEDIALP 593
                                    14        24        34        44        54        64        74        84       | -  |    104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    |    -|      284       294       304       314|        -|      334       344       354       364       374       384       394       404       414       424       434       444     |   -  |    464       474       484       494       504|        -         -    |  534       544       554       564       574       584         
                                                                                                                  92   97                                                                                                                                                                         269   275                                     315       325                                                                                                                          450    457                                             505                     529                                                                

   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 4CCA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CCA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CCA)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STXB2_HUMAN | Q15833)
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:0017075    syntaxin-1 binding    Interacting selectively and non-covalently with the SNAP receptor syntaxin-1.
    GO:0030348    syntaxin-3 binding    Interacting selectively and non-covalently with the SNAP receptor syntaxin-3.
biological process
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0001909    leukocyte mediated cytotoxicity    The directed killing of a target cell by a leukocyte.
    GO:0043312    neutrophil degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as proteases, lipases, and inflammatory mediators by a neutrophil.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0043304    regulation of mast cell degranulation    Any process that modulates the frequency, rate, or extent of mast cell degranulation.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0042582    azurophil granule    Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
    GO:0044194    cytolytic granule    A specialized secretory lysosome that is present in cells with cytolytic capability such as cytotoxic T lymphocytes and natural killer cells. Cytolytic granules mediate the storage and regulated excretion of lytic molecules for killing of target cells.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0042581    specific granule    Granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.
    GO:0070820    tertiary granule    A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells.

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