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(-) Description

Title :  SEC22B N-TERMINAL DOMAIN
 
Authors :  L. C. Gonzalez Jr. , W. I. Weis, R. H. Scheller
Date :  13 Apr 01  (Deposition) - 02 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Five-Stranded Anti-Parallel Beta Sheet, Alpha/Beta 3-Layer Sandwich, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. C. Gonzalez Jr. , W. I. Weis, R. H. Scheller
A Novel Snare N-Terminal Domain Revealed By The Crystal Structure Of Sec22B.
J. Biol. Chem. V. 276 24203 2001
PubMed-ID: 11309394  |  Reference-DOI: 10.1074/JBC.M101584200

(-) Compounds

Molecule 1 - VESICLE TRAFFICKING PROTEIN SEC22B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-9
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN (RESIDUES 2-127)
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:98 , HIS A:99 , LYS A:102 , HOH A:148 , GLN B:39 , ARG B:42 , HOH B:138BINDING SITE FOR RESIDUE GOL A 128
2AC2SOFTWAREGLN A:32 , SER A:35 , SER B:111 , HOH B:155BINDING SITE FOR RESIDUE GOL B 128

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LONGINPS50859 Longin domain profile.SC22B_MOUSE6-119
 
  2A:6-119
B:6-119
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LONGINPS50859 Longin domain profile.SC22B_MOUSE6-119
 
  1A:6-119
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LONGINPS50859 Longin domain profile.SC22B_MOUSE6-119
 
  1-
B:6-119

(-) Exons   (0, 0)

(no "Exon" information available for 1IFQ)

(-) 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:127
 aligned with SC22B_MOUSE | O08547 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
          SC22B_MOUSE     1 MVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYI 127
               SCOP domains d1ifqa_ A: Sec22b                                                                                                               SCOP domains
               CATH domains 1ifqA00 A:1-127  [code=3.30.450.50, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeeee......hhhhhhhhhhhhhhhhh........eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LONGIN  PDB: A:6-119 UniProt: 6-119                                                                               -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ifq A   1 SVLLTmIARVADGLPLAASmQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAmTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYI 127
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       
                                 6-MSE        20-MSE                                 59-MSE                                                                

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with SC22B_MOUSE | O08547 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:128
                             1                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119        
          SC22B_MOUSE     - -MVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYI 127
               SCOP domains d1ifqb_ B: Sec22b                                                                                                                SCOP domains
               CATH domains 1ifqB00 B:0-127  [code=3.30.450.50, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....eeeee......hhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------LONGIN  PDB: B:6-119 UniProt: 6-119                                                                               -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ifq B   0 GSVLLTmIARVADGLPLAASmQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAmTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYI 127
                                  |  9        19|       29        39        49        59        69        79        89        99       109       119        
                                  6-MSE        20-MSE                                 59-MSE                                                                

   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: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IFQ)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SC22B_MOUSE | O08547)
molecular function
    GO:0005484    SNAP receptor activity    Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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:0033043    regulation of organelle organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
    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:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SC22B_MOUSE | O085475vne 5vnf 5vng 5vnh 5vni 5vnj 5vnk 5vnl 5vnm 5vnn 5vno

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