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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DH AND PH-1 DOMAINS OF HUMAN FGD5
 
Authors :  Y. Shen, L. Nedyalkova, Y. Tong, W. Tempel, L. Crombet, C. H. Arrowsmith A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structur Genomics Consortium (Sgc)
Date :  27 Apr 10  (Deposition) - 23 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics Consortium, Dh Domain, Ph Domain, Sgc, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Shen, L. Nedyalkova, Y. Tong, W. Tempel, L. Crombet, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Dh And Ph-1 Domains Of Human Fgd5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FYVE, RHOGEF AND PH DOMAIN-CONTAINING PROTEIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)-V2R-PRARE2
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 889-1304
    GeneFGD5, ZFYVE23
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 23

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2UNX11Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3MPX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059801E941KFGD5_HUMANPolymorphism2307092AE941K

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DH_2PS50010 Dbl homology (DH) domain profile.FGD5_HUMAN892-1084  1A:892-1084
2PH_DOMAINPS50003 PH domain profile.FGD5_HUMAN1113-1207
1363-1461
  1A:1113-1205
-

(-) Exons   (0, 0)

(no "Exon" information available for 3MPX)

(-) 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:303
 aligned with FGD5_HUMAN | Q6ZNL6 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:316
                                   899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      
          FGD5_HUMAN    890 QSRALVIAQELLSSEKAYVEMLQHLNLDFHGAVMRALDDMDHEGRDTLAREELRQGLSELPAIHDLHQGILEELEERLSNWESQQKVADVFLAREQGFDHHATHILQFDRYLGLLSENCLHSPRLAAAVREFEQSVQGGSQTAKHRLLRVVQRLFQYQVLLTDYLNNLCPDSAEYDNTQGALSLISKVTDRANDSMEQGENLQKLVHIEHSVRGQGDLLQPGREFLKEGTLMKVTGKNRRPRHLFLMNDVLLYTYPQKDGKYRLKNTLAVANMKVSRPVMEKVPYALKIETSESCLMLSASSCAERDEWYGCLSRA 1205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.------hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhee...........eee..eeeeee..eeeeeeeeee..eeeeeee.....eeeeeeee.-----..........eeeee....eeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --DH_2  PDB: A:892-1084 UniProt: 892-1084                                                                                                                                                          ----------------------------PH_DOMAIN  PDB: A:1113-1205 UniProt: 1113-1207                                                PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mpx A  890 QSRALVIAQELLSSEKAYVEmLQHLNLDFHGAVmRALDDmDHE--DTLAREELRQGLSELPAIHDLHQGILEELEERLSNWESQQKVADVFLAREQGFDHHATHILQFDRYLGLLSENCLHSPRLAAAVREFEQS------TAKHRLLRVVQRLFQYQVLLTDYLNNLCPDSAEYDNTQGALSLISKVTDRANDSmEQGENLQKLVHIEHSVRGQGDLLQPGREFLKEGTLmKVTGKNRRPRHLFLmNDVLLYTYPQKDGKYRLKNTLAV-----SRPVmEKVPYALKIETSESCLmLSASSCAERDEWYGCLSRA 1205
                                   899       909|      919   |   929  |  | 939       949       959       969       979       989       999      1009      1019    |    - |    1039      1049      1059      1069      1079     |1089      1099      1109      1119 |    1129      1139      1149      1159     |1169      1179      1189      1199      
                                              910-MSE      923-MSE |  |  |                                                                                     1024   1031                                                  1085-MSE                            1121-MSE       1136-MSE               1159  1165   |             1186-MSE               
                                                                 929-MSE |                                                                                                                                                                                                                                      1169-MSE                                
                                                                    932  |                                                                                                                                                                                                                                                                              
                                                                       935                                                                                                                                                                                                                                                                              

   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 3MPX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MPX)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FGD5_HUMAN | Q6ZNL6)
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: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: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).
    GO:0031267    small GTPase binding    Interacting selectively and non-covalently with a small monomeric GTPase.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0046847    filopodium assembly    The assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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