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(-) Description

Title :  HUMAN STARD13 (DLC2) LIPID TRANSFER AND PROTEIN LOCALIZATION DOMAIN
 
Authors :  L. Lehtio, R. Busam, C. H. Arrowsmith, H. Berglund, R. Collins, L. G. Dah A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Ha L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kote M. Moche, P. Nordlund, T. Nyman, D. Ogg, J. Sagemark, P. Stenmark, M. Su A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, C. Persson, Str Genomics Consortium (Sgc)
Date :  07 May 07  (Deposition) - 15 May 07  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alpha And Beta Protein, Lipid Binding, Helix Swapping, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Thorsell, W. H. Lee, C. Persson, M. I. Siponen, M. Nilsson, R. D. Busam, T. Kotenyova, H. Schuler, L. Lehtio
Comparative Structural Analysis Of Lipid Binding Start Domains.
Plos One V. 6 19521 2011
PubMed-ID: 21738568  |  Reference-DOI: 10.1371/JOURNAL.PONE.0019521

(-) Compounds

Molecule 1 - STAR-RELATED LIPID TRANSFER PROTEIN 13
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: START DOMAIN
    Gene: STARD13, DLC2, GT650
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: STARD13, START DOMAIN-CONTAINING PROTEIN 13, 46H23.2, DELETED IN LIVER CANCER PROTEIN 2, RHO GTPASE-ACTIVATING PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2PSO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His B:907 -Thr B:908
2Thr B:908 -Tyr B:909

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STARTPS50848 START domain profile.STA13_HUMAN914-1082
 
 		  3A:914-1082
B:914-1082
C:914-1082
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STARTPS50848 START domain profile.STA13_HUMAN914-1082
 
 		  1A:914-1082
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STARTPS50848 START domain profile.STA13_HUMAN914-1082
 
 		  1-
B:914-1082
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STARTPS50848 START domain profile.STA13_HUMAN914-1082
 
 		  1-
-
C:914-1082

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003369341aENSE00002177288chr13:33859892-33859607286STA13_HUMAN1-57570--
1.4bENST000003369344bENSE00001798260chr13:33741759-3374168872STA13_HUMAN57-81250--
1.5ENST000003369345ENSE00001746318chr13:33739555-3373947482STA13_HUMAN81-108280--
1.7ENST000003369347ENSE00001619826chr13:33716510-3371644764STA13_HUMAN108-129220--
1.9ENST000003369349ENSE00000907354chr13:33704426-337030661361STA13_HUMAN130-5834540--
1.10ENST0000033693410ENSE00000907353chr13:33701683-33701510174STA13_HUMAN583-641590--
1.11ENST0000033693411ENSE00000907352chr13:33700377-33700218160STA13_HUMAN641-694540--
1.12ENST0000033693412ENSE00000907350chr13:33692400-33692202199STA13_HUMAN695-761670--
1.14bENST0000033693414bENSE00000907348chr13:33687068-33686858211STA13_HUMAN761-831710--
1.15bENST0000033693415bENSE00000907347chr13:33686029-33685915115STA13_HUMAN831-869390--
1.16ENST0000033693416ENSE00000907345chr13:33685044-33684823222STA13_HUMAN870-943743A:908-943
B:907-943
C:909-943		36
37
35
1.17ENST0000033693417ENSE00000907343chr13:33684227-33684010218STA13_HUMAN944-1016733A:944-1016
B:944-1016
C:944-1016		73
73
73
1.18ENST0000033693418ENSE00000907341chr13:33681071-33680895177STA13_HUMAN1016-1075603A:1016-1075
B:1016-1075
C:1016-1075 (gaps)		60
60
60
1.19aENST0000033693419aENSE00001872311chr13:33679847-336773072541STA13_HUMAN1075-1113393A:1075-1104
B:1075-1104
C:1075-1102		30
30
28

(-) 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:197
 aligned with STA13_HUMAN | Q9Y3M8 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:197
                                   917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097       
         STA13_HUMAN    908 TYLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQPL 1104
               SCOP domains d2psoa1 A:908-1104 Star-related lipid transfer protein 13                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...eee......eeeee.........eeeeeeee..hhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeee........eeeeeeeeee..hhhhheeeeeee...........ee..eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------START  PDB: A:914-1082 UniProt: 914-1082                                                                                                                                 ---------------------- PROSITE
           Transcript 1 (1) Exon 1.16  PDB: A:908-943           Exon 1.17  PDB: A:944-1016 UniProt: 944-1016                             ----------------------------------------------------------Exon 1.19a  PDB: A:1075-1104   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.18  PDB: A:1016-1075 UniProt: 1016-1075              ----------------------------- Transcript 1 (2)
                2pso A  908 TYLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQPL 1104
                                   917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097       


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with STA13_HUMAN | Q9Y3M8 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:198
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096        
         STA13_HUMAN    907 HTYLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQPL 1104
               SCOP domains d2psob_ B: Star-related lipid transfer protein 13                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..eeee......eeeee.........eeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee........eeeeeeeeee.......eeeeeee...........ee.eeeeeeeeeeee...eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------START  PDB: B:914-1082 UniProt: 914-1082                                                                                                                                 ---------------------- PROSITE
           Transcript 1 (1) Exon 1.16  PDB: B:907-943            Exon 1.17  PDB: B:944-1016 UniProt: 944-1016                             ----------------------------------------------------------Exon 1.19a  PDB: B:1075-1104   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------Exon 1.18  PDB: B:1016-1075 UniProt: 1016-1075              ----------------------------- Transcript 1 (2)
                2pso B  907 HTYLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQPL 1104
                                   916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096        


Chain C from PDB  Type:PROTEIN  Length:188
 aligned with STA13_HUMAN | Q9Y3M8 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:194
                                   918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098    
         STA13_HUMAN    909 YLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQ 1102
               SCOP domains d2psoc_ C: Star-related lipid transfer protein 13                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) START-2psoC01 C:909-1102                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) START-2psoC02 C:909-1102                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) START-2psoC03 C:909-1102                                                                                                                                                                           Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhh....eee......eeeeee.......eeeeeeee...hhhhhhhhhhh............eeeee....eeeeeeee........eeeeeeeeee.......eeeeeee...........ee.eeeeeeeee.------.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----START  PDB: C:914-1082 UniProt: 914-1082                                                                                                                                 -------------------- PROSITE
           Transcript 1 (1) Exon 1.16  PDB: C:909-943          Exon 1.17  PDB: C:944-1016 UniProt: 944-1016                             ----------------------------------------------------------Exon 1.19a  PDB: C:1075-1102 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.18  PDB: C:1016-1075 (gaps) UniProt: 1016-1075       --------------------------- Transcript 1 (2)
                2pso C  909 YLNHLIQGLQKEAKEKFKGWVTCSSTDNTDLAFKKVGDGNPLKLWKASVEVEAPPSVVLNRVLRERHLWDEDFVQWKVVETLDRQTEIYQYVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEEAQLLGGVRAVVMDSQYLIE------SRLTHICRIDLKGHSPEWYSKGFGHLCAAEVARIRNSFQ 1102
                                   918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048        |-     |1068      1078      1088      1098    
                                                                                                                                                                             1057   1064
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Bet_V_1_like (93)
(-)
Family: START (8)
(-)
Homo sapiens (Human) (6)
1aSTART-2psoC01C:909-1102
1bSTART-2psoC02C:909-1102
1cSTART-2psoC03C:909-1102

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (STA13_HUMAN | Q9Y3M8)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0043542    endothelial cell migration    The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0097498    endothelial tube lumen extension    Any endothelial tube morphogenesis process by which the tube is increased in length.
    GO:0090051    negative regulation of cell migration involved in sprouting angiogenesis    Any process that decreases the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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    His B:907 - Thr B:908   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        STA13_HUMAN | Q9Y3M8: 2h80 2jw2

(-) Related Entries Specified in the PDB File

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