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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAS-ASSOCIATION (RA) DOMAIN OF RALGDS
 
Authors :  Y. Shen, W. Tempel, H. Wang, Y. Tong, X. Guan, L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  29 Oct 09  (Deposition) - 17 Nov 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Structural Genomics Consortium, Sgc, Ras-Association Domain, Alternative Splicing, Guanine-Nucleotide Releasing Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shen, W. Tempel, H. Wang, Y. Tong, X. Guan, L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Ras-Association (Ra) Domain Of Ralgds
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 511693
    Gene: RALGDS, KIAA1308, RGF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RALGDS, RALGEF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3KH0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KH0)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RAPS50200 Ras-associating (RA) domain profile.GNDS_HUMAN798-885
 		  2A:798-885
B:798-885
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RAPS50200 Ras-associating (RA) domain profile.GNDS_HUMAN798-885
 		  2A:798-885
B:798-885
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RAPS50200 Ras-associating (RA) domain profile.GNDS_HUMAN798-885
 		  2A:798-885
B:798-885

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000003720503bENSE00001514306chr9:135996563-135996359205GNDS_HUMAN1-61610--
1.4ENST000003720504ENSE00001801549chr9:135987539-135987429111GNDS_HUMAN62-98370--
1.5ENST000003720505ENSE00001694768chr9:135985876-135985683194GNDS_HUMAN99-163650--
1.6aENST000003720506aENSE00001804795chr9:135985108-13598501396GNDS_HUMAN163-195330--
1.7aENST000003720507aENSE00001736419chr9:135984253-135984060194GNDS_HUMAN195-260660--
1.8aENST000003720508aENSE00001137115chr9:135983793-135983375419GNDS_HUMAN260-3991400--
1.9ENST000003720509ENSE00001137109chr9:135982687-135982472216GNDS_HUMAN400-471720--
1.10ENST0000037205010ENSE00001137104chr9:135982135-135982032104GNDS_HUMAN472-506350--
1.11ENST0000037205011ENSE00001137096chr9:135981403-13598131985GNDS_HUMAN506-534290--
1.12cENST0000037205012cENSE00001137089chr9:135979718-13597965069GNDS_HUMAN535-557230--
1.13bENST0000037205013bENSE00001137082chr9:135979220-13597913487GNDS_HUMAN558-586290--
1.14ENST0000037205014ENSE00000954148chr9:135978649-13597861733GNDS_HUMAN587-597110--
1.15ENST0000037205015ENSE00001137069chr9:135978287-135978166122GNDS_HUMAN598-638410--
1.16bENST0000037205016bENSE00001137061chr9:135977958-13597786396GNDS_HUMAN638-670330--
1.17aENST0000037205017aENSE00001137012chr9:135977526-135977325202GNDS_HUMAN670-737682A:787-792 (gaps)
B:787-792 (gaps)		11
11
1.17fENST0000037205017fENSE00002187251chr9:135977149-135976907243GNDS_HUMAN738-818812A:793-818
B:793-818		26
26
1.17kENST0000037205017kENSE00001720993chr9:135975769-135975655115GNDS_HUMAN819-857392A:819-857
B:819-857		39
39
1.17oENST0000037205017oENSE00001677413chr9:135974149-1359731071043GNDS_HUMAN857-914582A:857-892 (gaps)
B:857-893 (gaps)		36
37

(-) 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:102
 aligned with GNDS_HUMAN | Q12967 from UniProtKB/Swiss-Prot  Length:914

    Alignment length:170
                                   732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892
           GNDS_HUMAN   723 NISFVPESPDGQEKKFWESASQSSPETSGISSASSSTSSSSASTTPVAATRTHKRSVSGLCNSSSALPLYNQQVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMDKHNLEEEEPEDYELLQILSDDRKLKIPENANVFYAMNSTANYDFVLKKRTFTKGVKVK 892
               SCOP domains d3kh0     a                                                           _ A: automated matches                                                                               SCOP domains
               CATH domains 3kh0A     0                                                           0 A:787-892 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-----.-----------------------------------------------------------......eeeeeeeee....eeeeeeeee...hhhhhhhhhhhhh.....hhh.eeeeeeee..eeee.....hhhhhh......eeeeee...----.ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------RA  PDB: A:798-885 UniProt: 798-885                                                     ------- PROSITE
           Transcript 1 (1) Exon 1.17a     Exon 1.17f  PDB: A:793-818 UniProt: 738-818 [INCOMPLETE]                         Exon 1.17k  PDB: A:819-857             ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------Exon 1.17o  PDB: A:857-892 (gaps)    Transcript 1 (2)
                 3kh0 A 787 NLYFQ-----G-----------------------------------------------------------NQQVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMDKHNLEEEEPEDYELLQILSDDRKLKIPENANVFYAMNSTANYDFVLKKRTF----KVK 892
                                |    -|        -         -         -         -         -         -|      802       812       822       832       842       852       862       872       882  |    892
                              791   792                                                         793                                                                                         885  890  


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with GNDS_HUMAN | Q12967 from UniProtKB/Swiss-Prot  Length:914

    Alignment length:171
                                   732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892 
           GNDS_HUMAN   723 NISFVPESPDGQEKKFWESASQSSPETSGISSASSSTSSSSASTTPVAATRTHKRSVSGLCNSSSALPLYNQQVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMDKHNLEEEEPEDYELLQILSDDRKLKIPENANVFYAMNSTANYDFVLKKRTFTKGVKVKH 893
               SCOP domains d3kh0     b                                                           _ B: automated matches                                                                                SCOP domains
               CATH domains 3kh0B     0                                                           0 B:787-893 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                        CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------RA-3kh0B01 B:798-885                                                                    -------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------RA-3kh0B02 B:798-885                                                                    -------- Pfam domains (2)
         Sec.struct. author .....-----.-----------------------------------------------------------......eeeeeeeee....eeeeeeeee...hhhhhhhhhhhhh.....hhh.eeeeee.....eee.....hhhhhh......eeeeee...--..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------RA  PDB: B:798-885 UniProt: 798-885                                                     -------- PROSITE
           Transcript 1 (1) Exon 1.17a     Exon 1.17f  PDB: B:793-818 UniProt: 738-818 [INCOMPLETE]                         Exon 1.17k  PDB: B:819-857             ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------Exon 1.17o  PDB: B:857-893 (gaps)     Transcript 1 (2)
                 3kh0 B 787 NLYFQ-----G-----------------------------------------------------------NQQVGDCCIIRVSLDVDNGNMYKSILVTSQDKAPAVIRKAMDKHNLEEEEPEDYELLQILSDDRKLKIPENANVFYAMNSTANYDFVLKKRTF--GVKVKH 893
                                |    -|        -         -         -         -         -         -|      802       812       822       832       842       852       862       872       882  |  | 892 
                              791   792                                                         793                                                                                         885  |     
                                                                                                                                                                                               888
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)
(-)
Family: RA (7)
(-)
Homo sapiens (Human) (4)
1aRA-3kh0B01B:798-885
1bRA-3kh0B02B:798-885

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GNDS_HUMAN | Q12967)
molecular function
    GO:0030695    GTPase regulator activity    Modulates the rate of GTP hydrolysis by a GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. 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: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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    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.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3kh0
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 Related Entries

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

UniProtKB/Swiss-Prot
        GNDS_HUMAN | Q12967: 1rax 2b3a 2rgf

(-) Related Entries Specified in the PDB File

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