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(-) Description

Title :  SOLUTION STRUCTURE OF LARG PDZ DOMAIN
 
Authors :  J. Liu, H. Huang, Q. Hu
Date :  22 Jan 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nerve System Development, Actin Reorganization, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, H. Huang
Solution Structure And Dynamics Of The Larg Pdz Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 12
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B (+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LARG PROTEIN, LEUKEMIA-ASSOCIATED RHOGEF

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2OMJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OMJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ARHGC_HUMAN72-136  1A:10-74

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003978431aENSE00002172160chr11:120207787-120207984198ARHGC_HUMAN1-11110--
1.3bENST000003978433bENSE00001364534chr11:120276827-12027685024ARHGC_HUMAN11-1990--
1.4aENST000003978434aENSE00000990332chr11:120278447-12027853286ARHGC_HUMAN19-48301A:1-33
1.4cENST000003978434cENSE00001530577chr11:120280103-12028015957ARHGC_HUMAN48-67201A:4-52
1.5ENST000003978435ENSE00000990335chr11:120291462-12029156099ARHGC_HUMAN67-100341A:5-3834
1.6ENST000003978436ENSE00001125958chr11:120292512-12029256150ARHGC_HUMAN100-116171A:38-5417
1.7ENST000003978437ENSE00000990338chr11:120295067-12029512458ARHGC_HUMAN117-136201A:55-7420
1.8ENST000003978438ENSE00000990339chr11:120298778-120298956179ARHGC_HUMAN136-195601A:74-8916
1.9ENST000003978439ENSE00000990340chr11:120300149-12030022678ARHGC_HUMAN196-221260--
1.10ENST0000039784310ENSE00000990342chr11:120300421-120300540120ARHGC_HUMAN222-261400--
1.11ENST0000039784311ENSE00000990343chr11:120302480-120302620141ARHGC_HUMAN262-308470--
1.12ENST0000039784312ENSE00001205806chr11:120308017-12030809175ARHGC_HUMAN309-333250--
1.13bENST0000039784313bENSE00001205799chr11:120310838-12031093093ARHGC_HUMAN334-364310--
1.14ENST0000039784314ENSE00001205793chr11:120312416-120312526111ARHGC_HUMAN365-401370--
1.15ENST0000039784315ENSE00001205786chr11:120312813-12031291199ARHGC_HUMAN402-434330--
1.16ENST0000039784316ENSE00001205988chr11:120316131-12031617343ARHGC_HUMAN435-449150--
1.17ENST0000039784317ENSE00001205778chr11:120317112-120317217106ARHGC_HUMAN449-484360--
1.18aENST0000039784318aENSE00001125859chr11:120317657-120317794138ARHGC_HUMAN484-530470--
1.19ENST0000039784319ENSE00000990353chr11:120318583-12031861533ARHGC_HUMAN530-541120--
1.20ENST0000039784320ENSE00000990354chr11:120318943-120319057115ARHGC_HUMAN541-579390--
1.21bENST0000039784321bENSE00001205763chr11:120319818-120319923106ARHGC_HUMAN580-615360--
1.22cENST0000039784322cENSE00001125819chr11:120322221-120322433213ARHGC_HUMAN615-686720--
1.23ENST0000039784323ENSE00000990358chr11:120327827-120327959133ARHGC_HUMAN686-730450--
1.24cENST0000039784324cENSE00000990359chr11:120328430-12032846536ARHGC_HUMAN730-742130--
1.24dENST0000039784324dENSE00000990360chr11:120328789-120328943155ARHGC_HUMAN742-794530--
1.24fENST0000039784324fENSE00001125791chr11:120329883-120330029147ARHGC_HUMAN794-843500--
1.25ENST0000039784325ENSE00000990363chr11:120331381-12033146686ARHGC_HUMAN843-871290--
1.26bENST0000039784326bENSE00000990365chr11:120335946-120336071126ARHGC_HUMAN872-913420--
1.27ENST0000039784327ENSE00000990366chr11:120337903-120338017115ARHGC_HUMAN914-952390--
1.28ENST0000039784328ENSE00000990367chr11:120339997-120340097101ARHGC_HUMAN952-985340--
1.29ENST0000039784329ENSE00000990368chr11:120343759-12034383678ARHGC_HUMAN986-1011260--
1.30ENST0000039784330ENSE00001125877chr11:120345269-12034534476ARHGC_HUMAN1012-1037260--
1.31ENST0000039784331ENSE00001430984chr11:120346049-120346216168ARHGC_HUMAN1037-1093570--
1.32bENST0000039784332bENSE00001402131chr11:120347370-12034745788ARHGC_HUMAN1093-1122300--
1.33bENST0000039784333bENSE00001125767chr11:120347928-12034801487ARHGC_HUMAN1122-1151300--
1.34aENST0000039784334aENSE00000990377chr11:120348156-12034823580ARHGC_HUMAN1151-1178280--
1.35ENST0000039784335ENSE00000990378chr11:120348865-120349098234ARHGC_HUMAN1178-1256790--
1.36bENST0000039784336bENSE00001125757chr11:120350669-120351139471ARHGC_HUMAN1256-14131580--
1.37ENST0000039784337ENSE00001401289chr11:120351969-120352285317ARHGC_HUMAN1413-15181060--
1.38ENST0000039784338ENSE00001369958chr11:120355147-12035521670ARHGC_HUMAN1519-1542240--
1.39bENST0000039784339bENSE00001364735chr11:120355776-1203606454870ARHGC_HUMAN1542-154430--

(-) Sequences/Alignments

NMR Structure
   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:89
 aligned with ARHGC_HUMAN | Q9NZN5 from UniProtKB/Swiss-Prot  Length:1544

    Alignment length:112
                                    49        59        69        79        89        99       109       119       129       139       149  
          ARHGC_HUMAN    40 ASHDFDPTDSSSKKTKSSSEESRSEIYGLVQRCVIIQKDDNGFGLTVSGDNPVFVQSVKEDGAAMRAGVQTGDRIIKVNGTLVTHSNHLEVVKLIKSGSYVALTVQGRPPGS 151
               SCOP domains d2o                       mja_ A: automated matches                                                              SCOP domains
               CATH domains 2om                       jA00 A:1-89  [code=2.30.42.10, no name defined]                                        CATH domains
               Pfam domains ---------------------------------PDZ-2omjA01 A:11-83                                                      ------ Pfam domains
         Sec.struct. author ...-----------------------....eeeeeee........eee.....eeee....hhhhhhh....eeeeee........hhhhhhhhhhh..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------PDZ  PDB: A:10-74 UniProt: 72-136                                --------------- PROSITE
           Transcript 1 (1) Exon 1.4a------------------Exon 1.5  PDB: A:5-38             ----------------Exon 1.7            --------------- Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.4c  PDB: A:4---------------------------------Exon 1.6         -------------------Exon 1.8         Transcript 1 (2)
                 2omj A   1 GSH-----------------------MGLVQRCVIIQKDDNGFGLTVSGDNPVFVQSVKEDGAAMRAGVQTGDRIIKVNGTLVTHSNHLEVVKLIKSGSYVALTVQGRPPGS  89
                              |      -         -      |  7        17        27        37        47        57        67        77        87  
                              3                       4
   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, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (ARHGC_HUMAN | Q9NZN5)
molecular function
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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: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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
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: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.
    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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        ARHGC_HUMAN | Q9NZN5: 1txd 1x86 2os6

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