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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN INTERSECTIN 2 C2 DOMAIN
 
Authors :  Y. Shen, W. Tempel, Y. Tong, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bou J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium
Date :  24 Sep 09  (Deposition) - 06 Oct 09  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A
Keywords :  C2 Domain, Structural Genomics Consortium (Sgc), Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shen, W. Tempel, Y. Tong, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Intersectin 2 C2 Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERSECTIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-V2R PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1173-1664, C2 DOMAIN
    Gene: ITSN2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3JZY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JZY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:1615 -Pro A:1616

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JZY)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.ITSN2_HUMAN1570-1652  1A:1542-1624

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003551231aENSE00001820402chr2:24583583-24583173411ITSN2_HUMAN-00--
1.2bENST000003551232bENSE00002171861chr2:24550984-2455092164ITSN2_HUMAN1-11110--
1.5ENST000003551235ENSE00001764011chr2:24538093-2453800193ITSN2_HUMAN11-42320--
1.6ENST000003551236ENSE00001720994chr2:24536392-2453632964ITSN2_HUMAN42-63220--
1.7ENST000003551237ENSE00001709424chr2:24535244-24535081164ITSN2_HUMAN63-118560--
1.9ENST000003551239ENSE00001771235chr2:24533561-24533358204ITSN2_HUMAN118-186690--
1.10bENST0000035512310bENSE00000722102chr2:24533249-2453315397ITSN2_HUMAN186-218330--
1.12ENST0000035512312ENSE00000808873chr2:24531625-24531486140ITSN2_HUMAN218-265480--
1.13ENST0000035512313ENSE00000722299chr2:24526731-2452666864ITSN2_HUMAN265-286220--
1.14ENST0000035512314ENSE00000722350chr2:24524971-24524834138ITSN2_HUMAN286-332470--
1.15ENST0000035512315ENSE00000808870chr2:24524108-2452402386ITSN2_HUMAN332-361300--
1.16ENST0000035512316ENSE00000722427chr2:24523040-24522778263ITSN2_HUMAN361-448880--
1.17ENST0000035512317ENSE00000722490chr2:24521683-24521534150ITSN2_HUMAN449-498500--
1.18aENST0000035512318aENSE00000722555chr2:24518673-24518533141ITSN2_HUMAN499-545470--
1.19aENST0000035512319aENSE00002183816chr2:24516644-2451655788ITSN2_HUMAN546-575300--
1.20bENST0000035512320bENSE00001620600chr2:24509220-24509081140ITSN2_HUMAN575-621470--
1.21ENST0000035512321ENSE00001679214chr2:24507712-2450763281ITSN2_HUMAN622-648270--
1.22ENST0000035512322ENSE00001705683chr2:24498718-24498582137ITSN2_HUMAN649-694460--
1.23ENST0000035512323ENSE00001650641chr2:24494810-24494635176ITSN2_HUMAN694-753600--
1.24ENST0000035512324ENSE00001605766chr2:24493637-2449354098ITSN2_HUMAN753-785330--
1.25ENST0000035512325ENSE00001768638chr2:24484611-24484430182ITSN2_HUMAN786-846610--
1.26ENST0000035512326ENSE00001642410chr2:24484119-24483975145ITSN2_HUMAN846-894490--
1.27ENST0000035512327ENSE00001784679chr2:24480962-24480757206ITSN2_HUMAN895-963690--
1.28ENST0000035512328ENSE00001630907chr2:24477300-2447723665ITSN2_HUMAN963-985230--
1.29ENST0000035512329ENSE00001729710chr2:24475380-24475214167ITSN2_HUMAN985-1040560--
1.30ENST0000035512330ENSE00001696254chr2:24471751-2447170646ITSN2_HUMAN1041-1056160--
1.31aENST0000035512331aENSE00001747856chr2:24471619-24471498122ITSN2_HUMAN1056-1096410--
1.32ENST0000035512332ENSE00001629269chr2:24469762-2446966697ITSN2_HUMAN1097-1129330--
1.33ENST0000035512333ENSE00001740845chr2:24469189-24468998192ITSN2_HUMAN1129-1193650--
1.35aENST0000035512335aENSE00001785423chr2:24443935-24443814122ITSN2_HUMAN1193-1233410--
1.36ENST0000035512336ENSE00001775662chr2:24440882-24440776107ITSN2_HUMAN1234-1269360--
1.37ENST0000035512337ENSE00001690566chr2:24439101-24438918184ITSN2_HUMAN1269-1330620--
1.38ENST0000035512338ENSE00001665782chr2:24435617-2443551999ITSN2_HUMAN1331-1363330--
1.39ENST0000035512339ENSE00001772990chr2:24433816-24433649168ITSN2_HUMAN1364-1419560--
1.40bENST0000035512340bENSE00001674611chr2:24432902-24432687216ITSN2_HUMAN1420-1491720--
1.41ENST0000035512341ENSE00001615807chr2:24432090-24431969122ITSN2_HUMAN1492-1532410--
1.42aENST0000035512342aENSE00001755618chr2:24431188-2443110683ITSN2_HUMAN1532-1560290--
1.44cENST0000035512344cENSE00001625120chr2:24428166-2442808384ITSN2_HUMAN1560-1588291A:1540-156021
1.45bENST0000035512345bENSE00001636642chr2:24427287-24427114174ITSN2_HUMAN1588-1646591A:1560-161859
1.45fENST0000035512345fENSE00001486636chr2:24426652-24425733920ITSN2_HUMAN1646-1697521A:1618-166346

(-) 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:124
 aligned with A6H8W8_HUMAN | A6H8W8 from UniProtKB/TrEMBL  Length:1669

    Alignment length:124
                                  1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659    
        A6H8W8_HUMAN   1540 IGRLMVHVIEATELKACKPNGKSNPYCEISMGSQSYTTRTIQDTLNPKWNFNCQFFIKDLYQDVLCLTLFDRDQFSPDDFLGRTEIPVAKIRTEQESKGPMTRRLLLHEVPTGEVWVRFDLQLF 1663
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---C2-3jzyA01 A:1543-1624                                                            --------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee............eeeeeee..eeee..........eeeeeeeeee......eeeeeeee........eeeeeeeehhhhhhhhhhhh...eeee.......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                3jzy A 1540 IGRLMVHVIEATELKACKPNGKSNPYCEISMGSQSYTTRTIQDTLNPKWNFNCQFFIKDLYQDVLCLTLFDRDQFSPDDFLGRTEIPVAKIRTEQESKGPMTRRLLLHEVPTGEVWVRFDLQLF 1663
                                  1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659    


Chain A from PDB  Type:PROTEIN  Length:124
 aligned with ITSN2_HUMAN | Q9NZM3 from UniProtKB/Swiss-Prot  Length:1697

    Alignment length:124
                                  1577      1587      1597      1607      1617      1627      1637      1647      1657      1667      1677      1687    
         ITSN2_HUMAN   1568 IGRLMVHVIEATELKACKPNGKSNPYCEISMGSQSYTTRTIQDTLNPKWNFNCQFFIKDLYQDVLCLTLFDRDQFSPDDFLGRTEIPVAKIRTEQESKGPMTRRLLLHEVPTGEVWVRFDLQLF 1691
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---C2-3jzyA01 A:1543-1624                                                            --------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee............eeeeeee..eeee..........eeeeeeeeee......eeeeeeee........eeeeeeeehhhhhhhhhhhh...eeee.......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --C2  PDB: A:1542-1624 UniProt: 1570-1652                                            --------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.44c           ---------------------------------------------------------Exon 1.45f  PDB: A:1618-1663 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.45b  PDB: A:1560-1618 UniProt: 1588-1646            --------------------------------------------- Transcript 1 (2)
                3jzy A 1540 IGRLMVHVIEATELKACKPNGKSNPYCEISMGSQSYTTRTIQDTLNPKWNFNCQFFIKDLYQDVLCLTLFDRDQFSPDDFLGRTEIPVAKIRTEQESKGPMTRRLLLHEVPTGEVWVRFDLQLF 1663
                                  1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659
   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 3JZY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: C2 (71)
(-)
Family: C2 (34)
(-)
Homo sapiens (Human) (15)
1aC2-3jzyA01A:1543-1624

(-) Gene Ontology  (14, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6H8W8_HUMAN | A6H8W8)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
biological process
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.

Chain A   (ITSN2_HUMAN | Q9NZM3)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
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: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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1903861    positive regulation of dendrite extension    Any process that activates or increases the frequency, rate or extent of dendrite extension.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        A6H8W8_HUMAN | A6H8W8: 3gf9
        ITSN2_HUMAN | Q9NZM3: 1j3t 1udl 1ue9 1uff 1uhf 3gf9 4iio

(-) Related Entries Specified in the PDB File

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