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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF LEUKEMIA-ASSOCIATED RHOGEF
 
Authors :  R. Kristelly, G. Gao, J. J. Tesmer
Date :  03 Jul 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A
Keywords :  Helical Bundle (Dh), Beta Sandwich (Ph), Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Kristelly, G. Gao, J. J. Tesmer
Structural Determinants Of Rhoa Binding And Nucleotide Exchange In Leukemia-Associated Rho Guanine-Nucleotide Exchange Factor.
J. Biol. Chem. V. 279 47352 2004
PubMed-ID: 15331592  |  Reference-DOI: 10.1074/JBC.M406056200

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 12
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDH/PH DOMAINS
    GeneARHGEF12, LARG, KIAA0382
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUKEMIA-ASSOCIATED RHOGEF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1TXD)

(-) Sites  (0, 0)

(no "Site" information available for 1TXD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TXD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TXD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020191Y973FARHGC_HUMANPolymorphism2305013AF973F

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DH_2PS50010 Dbl homology (DH) domain profile.ARHGC_HUMAN787-977  1A:787-977
2DH_1PS00741 Dbl homology (DH) domain signature.ARHGC_HUMAN926-951  1A:926-951
3PH_DOMAINPS50003 PH domain profile.ARHGC_HUMAN1019-1132  1A:1019-1132

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003978431aENSE00002172160chr11:120207787-120207984198ARHGC_HUMAN1-11110--
1.3bENST000003978433bENSE00001364534chr11:120276827-12027685024ARHGC_HUMAN11-1990--
1.4aENST000003978434aENSE00000990332chr11:120278447-12027853286ARHGC_HUMAN19-48300--
1.4cENST000003978434cENSE00001530577chr11:120280103-12028015957ARHGC_HUMAN48-67200--
1.5ENST000003978435ENSE00000990335chr11:120291462-12029156099ARHGC_HUMAN67-100340--
1.6ENST000003978436ENSE00001125958chr11:120292512-12029256150ARHGC_HUMAN100-116170--
1.7ENST000003978437ENSE00000990338chr11:120295067-12029512458ARHGC_HUMAN117-136200--
1.8ENST000003978438ENSE00000990339chr11:120298778-120298956179ARHGC_HUMAN136-195600--
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_HUMAN742-794531A:766-79429
1.24fENST0000039784324fENSE00001125791chr11:120329883-120330029147ARHGC_HUMAN794-843501A:794-84350
1.25ENST0000039784325ENSE00000990363chr11:120331381-12033146686ARHGC_HUMAN843-871291A:843-87129
1.26bENST0000039784326bENSE00000990365chr11:120335946-120336071126ARHGC_HUMAN872-913421A:872-91342
1.27ENST0000039784327ENSE00000990366chr11:120337903-120338017115ARHGC_HUMAN914-952391A:914-95239
1.28ENST0000039784328ENSE00000990367chr11:120339997-120340097101ARHGC_HUMAN952-985341A:952-98534
1.29ENST0000039784329ENSE00000990368chr11:120343759-12034383678ARHGC_HUMAN986-1011261A:986-1011 (gaps)26
1.30ENST0000039784330ENSE00001125877chr11:120345269-12034534476ARHGC_HUMAN1012-1037261A:1012-103726
1.31ENST0000039784331ENSE00001430984chr11:120346049-120346216168ARHGC_HUMAN1037-1093571A:1037-1092 (gaps)56
1.32bENST0000039784332bENSE00001402131chr11:120347370-12034745788ARHGC_HUMAN1093-1122301A:1094-112229
1.33bENST0000039784333bENSE00001125767chr11:120347928-12034801487ARHGC_HUMAN1122-1151301A:1122-113817
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

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:352
 aligned with ARHGC_HUMAN | Q9NZN5 from UniProtKB/Swiss-Prot  Length:1544

    Alignment length:373
                                   775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135   
         ARHGC_HUMAN    766 PPNWQQLVSREVLLGLKPCEIKRQEVINELFYTERAHVRTLKVLDQVFYQRVSREGILSPSELRKIFSNLEDILQLHIGLNEQMKAVRKRNETSVIDQIGEDLLTWFSGPGEEKLKHAAATFCSNQPFALEMIKSRQKKDSRFQTFVQDAESNPLCRRLQLKDIIPTQMQRLTKYPLLLDNIAKYTEWPTEREKVKKAADHCRQILNYVNQAVKEAENKQRLEDYQRRLDTSSLKLSEYPNVEELRNLDLTKRKMIHEGPLVWKVNRDKTIDLYTLLLEDILVLLQKQDDRLVLRCHSKILASTADSKHTFSPVIKLSTVLVRQVATDNKALFVISMSDNGAQIYELVAQTVSEKTVWQDLICRMAASVKEQS 1138
               SCOP domains d1txda1 A:766-999 Rho guanine nucleotide exchange factor 12                                                                                                                                                                                      -------------d1txda2 A:1020-1133 Rho guanine nucleotide              exchange factor 1 2                                       ----- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1tx       dA02 A:997-1138 Pleckstrin-homology domain (PH domain)/             Phosphotyrosine-bi nding domain (PTB)                            CATH domains
               Pfam domains -------------------------RhoGEF-1txdA01 A:791-976                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....-------hhhhhh.hhhhh.eeeeeeeeee........eeeeee..eeeeeeee..eee...-------------....eee...eeeee...-..eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------DH_2  PDB: A:787-977 UniProt: 787-977                                                                                                                                                          -----------------------------------------PH_DOMAIN  PDB: A:1019-1132 UniProt: 1019-1132                                                                    ------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------DH_1  PDB: A:926-951      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.24d  PDB: A:766-794   ------------------------------------------------Exon 1.25  PDB: A:843-871    Exon 1.26b  PDB: A:872-913                Exon 1.27  PDB: A:914-952              ---------------------------------Exon 1.29                 Exon 1.30  PDB: A:1012-103-------------------------------------------------------Exon 1.32b  PDB: A:1094-1122  ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.24f  PDB: A:794-843 UniProt: 794-843       ------------------------------------------------------------------------------------------------------------Exon 1.28  PDB: A:952-985         ---------------------------------------------------Exon 1.31  PDB: A:1037-1092 (gaps) UniProt: 1037-1093    ----------------------------Exon 1.33b        Transcript 1 (2)
                1txd A  766 PPNWQQLVSREVLLGLKPCEIKRQEVINELFYTERAHVRTLKVLDQVFYQRVSREGILSPSELRKIFSNLEDILQLHIGLNEQMKAVRKRNETSVIDQIGEDLLTWFSGPGEEKLKHAAATFCSNQPFALEMIKSRQKKDSRFQTFVQDAESNPLCRRLQLKDIIPTQMQRLTKYPLLLDNIAKYTEWPTEREKVKKAADHCRQILNFVNQAVKEAENKQRLEDYQRRLDTSSL-------VEELRNLDLTKRKMIHEGPLVWKVNRDKTIDLYTLLLEDILVLLQKQDDRLVLRC-------------TFSPVIKLSTVLVRQVAT-NKALFVISMSDNGAQIYELVAQTVSEKTVWQDLICRMAASVKEQS 1138
                                   775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995   |     - |    1015      1025      1035      1045      1055     |   -      1075      1085      1095      1105      1115      1125      1135   
                                                                                                                                                                                                                                                                   999    1007                                                  1061          1075             1092 |                                            
                                                                                                                                                                                                                                                                                                                                                                 1094                                            

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(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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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHGC_HUMAN | Q9NZN51x86 2omj 2os6

(-) Related Entries Specified in the PDB File

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