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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF MSP DOMAIN
 
Authors :  J. Shi, S. Lua, J. Song
Date :  06 Aug 09  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vapb Msp, Alternative Splicing, Amyotrophic Lateral Sclerosis, Cell Membrane, Coiled Coil, Disease Mutation, Host-Virus Interaction, Membrane, Neurodegeneration, Phosphoprotein, Transmembrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Shi, S. Lua, J. S. Tong, J. Song
Elimination Of The Native Structure And Solubility Of The Hvapb Msp Domain By The Pro56Ser Mutation That Causes Amyotrophic Lateral Sclerosis.
Biochemistry V. 49 3887 2010
PubMed-ID: 20377183  |  Reference-DOI: 10.1021/BI902057A

(-) Compounds

Molecule 1 - VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN B/C
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET32A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentVAPB MSP DOMAIN, UNP RESIDUES 1-125
    GeneUNQ484/PRO983, VAPB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN VAP-B MSP DOMAIN, VAMP-ASSOCIATED PROTEIN B/C, VAMP- B/VAMP-C, VAP-B/VAP-C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3IKK)

(-) Sites  (0, 0)

(no "Site" information available for 3IKK)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:53 -B:53

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Met A:1 -Ala A:2
2Glu A:11 -Pro A:12
3Gly A:20 -Pro A:21
4Arg A:55 -Pro A:56
5Ala B:2 -Lys B:3
6Glu B:11 -Pro B:12
7Gly B:20 -Pro B:21
8Arg B:55 -Pro B:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067964T46IVAPB_HUMANDisease (ALS8)281875284A/BT46I
2UniProtVAR_026743P56SVAPB_HUMANDisease (SMAPAD)74315431A/BP56S

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MSPPS50202 Major sperm protein (MSP) domain profile.VAPB_HUMAN7-124
 
  2A:7-124
B:7-124

(-) Exons   (0, 0)

(no "Exon" information available for 3IKK)

(-) 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:125
 aligned with VAPB_HUMAN | O95292 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           VAPB_HUMAN     1 MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFEL 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eeeee......eeeeeeee......eeeeeee.....eeee..eeee....eeeeeeee..............eeeeeee....................eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------I---------S--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MSP  PDB: A:7-124 UniProt: 7-124                                                                                      - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikk A   1 MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFEL 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with VAPB_HUMAN | O95292 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           VAPB_HUMAN     1 MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFEL 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eeeee......eeeeeeee......eeeeeee.....eeee..eeee....eeeeeeee..............eeeeeee.......................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------I---------S--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MSP  PDB: B:7-124 UniProt: 7-124                                                                                      - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikk B   1 MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFEL 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

   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 3IKK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IKK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IKK)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VAPB_HUMAN | O95292)
molecular function
    GO:0033149    FFAT motif binding    Interacting selectively and non-covalently with the FFAT motif, a short motif containing diphenylalanine in an acidic tract that targets proteins to the cytosolic surface of the ER and to the nuclear membrane by binding directly to members of the VAP (VAMP-associated protein) protein family.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0090114    COPII-coated vesicle budding    The evagination of an endoplasmic reticulum membrane, resulting in formation of a COPII-coated vesicle.
    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:0006987    activation of signaling protein activity involved in unfolded protein response    The conversion of a specific protein, possessing protein kinase and endoribonuclease activities, to an active form as a result of signaling via the unfolded protein response.
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0007029    endoplasmic reticulum organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0044830    modulation by host of viral RNA genome replication    A process in which a host organism modulates the frequency, rate or extent of viral RNA genome replication.
    GO:0019048    modulation by virus of host morphology or physiology    The process in which a virus effects a change in the structure or processes of its host organism.
    GO:0044828    negative regulation by host of viral genome replication    A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral genome replication.
    GO:0044790    negative regulation by host of viral release from host cell    A process in which a host organism stops, prevents or reduces the frequency, rate or extent of the release of a virus with which it is infected, from its cells.
    GO:0046725    negative regulation by virus of viral protein levels in host cell    Any process where the infecting virus reduces the levels of viral proteins in a cell.
    GO:0044829    positive regulation by host of viral genome replication    A process in which a host organism activates or increases the frequency, rate or extent of viral genome replication.
    GO:0044791    positive regulation by host of viral release from host cell    A process in which a host organism activates or increases the frequency, rate or extent of the release of a virus with which it is infected, from its cells.
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0030148    sphingolipid biosynthetic process    The chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
    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: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: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:0070971    endoplasmic reticulum exit site    An endoplasmic reticulum part at which COPII-coated vesicles are produced.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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    Ala B:2 - Lys B:3   [ RasMol ]  
    Arg A:55 - Pro A:56   [ RasMol ]  
    Arg B:55 - Pro B:56   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        VAPB_HUMAN | O952922mdk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3IKK)