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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF HUMAN RHOPHILIN-2
 
Authors :  A. C. W. Pike, G. Kochan, Z. Sun, N. Shafqat, E. S. Pilka, A. Roos, J. Elkins, N. Burgess-Brown, J. W. Murray, F. Von Delft, M. Wikstrom, A. Edwards, C. H. Arrowsmith, C. Bountra, U. Oppermann
Date :  29 Apr 08  (Deposition) - 15 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Scaffold Protein, Rho Gtpase Binding, Protein-Binding, Rhob, Nitration, Cytoplasm, Pdz Domain, Casp8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. W. Pike, G. Kochan, Z. Sun, N. Shafqat, E. S. Pilka, A. Roos, J. Elkins, N. Burgess-Brown, J. W. Murray, F. Von Delft, M. Wikstrom, A. Edwards, C. H. Arrowsmith, C. Bountra, U. Oppermann
Crystal Structure Of The Pdz Domain Of Human Rhophilin-2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RHOPHILIN-2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Fragment: PDZ DOMAIN, RESIDUES 514-595
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GTP-RHO-BINDING PROTEIN 2,76 KDA RHOB EFFECTOR PROTEIN, P76RBE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2VSV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:534 -Pro A:535
2Ala B:534 -Pro B:535

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VSV)

(-) Exons   (0, 0)

(no "Exon" information available for 2VSV)

(-) 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:97
 aligned with RHPN2_HUMAN | Q8IUC4 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:225
                                   379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589     
          RHPN2_HUMAN   370 KPGTDLDHQEKCLSQLYDHMPEGLTPLATLKNDQQRRQLGKSHLRRAMAHHEESVREASLCKKLRSIEVLQKVLCAAQERSRLTYAQHQEEDDLLNLIDAPSVVAKTEQEVDIILPQFSKLTVTDFFQKLGPLSVFSANKRWTPPRSIRFTAEEGDLGFTLRGNAPVQVHFLDPYCSASVAGAREGDYIVSIQLVDCKWLTLSEVMKLLKSFGEDEIEMKVVSLL 594
               SCOP domains d2vsva_ A:      a                                                                                                             utom              ated matches                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh-----hh-------------------------------------------------------------------------------------------------------------hhhh--------------.eeeee.hhhhh..eeee.....eeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsv A -15 SSGVDLGTEN-----LY-------------------------------------------------------------------------------------------------------------FQSM--------------PRSIRFTAEEGDLGFTLRGNAPVQVHFLDPYCSASVAGAREGDYIVSIQLVDCKWLTLSEVMKLLKSFGEDEIEMKVVSLL 594
                                    -6     ||  -         -         -         -         -         -         -         -         -         -         -      |  0         -    |  519       529       539       549       559       569       579       589     
                                    -6    -5|                                                                                                            -3  0            514                                                                                
                                           -4                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with RHPN2_HUMAN | Q8IUC4 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:246
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588      
          RHPN2_HUMAN   349 AHHYAALAHYFTAILLIDHQVKPGTDLDHQEKCLSQLYDHMPEGLTPLATLKNDQQRRQLGKSHLRRAMAHHEESVREASLCKKLRSIEVLQKVLCAAQERSRLTYAQHQEEDDLLNLIDAPSVVAKTEQEVDIILPQFSKLTVTDFFQKLGPLSVFSANKRWTPPRSIRFTAEEGDLGFTLRGNAPVQVHFLDPYCSASVAGAREGDYIVSIQLVDCKWLTLSEVMKLLKSFGEDEIEMKVVSLL 594
               SCOP domains d2vs              vb_ B: automa     te                                                                                                             d ma              tches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------BRO1----------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------BRO1----------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....--------------.....hhhhhhhh-----hh-------------------------------------------------------------------------------------------------------------hhhh--------------.eeeee.hhhhh..eeee.....eeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vsv B -22 MHHH--------------HHHSSGVDLGTEN-----LY-------------------------------------------------------------------------------------------------------------FQSM--------------PRSIRFTAEEGDLGFTLRGNAPVQVHFLDPYCSASVAGAREGDYIVSIQLVDCKWLTLSEVMKLLKSFGEDEIEMKVVSLL 594
                               |     -       -17        -7|     || -         -         -         -         -         -         -         -         -         -         -       |-1|        -     | 518       528       538       548       558       568       578       588      
                             -19            -18          -6    -5|                                                                                                            -3  0            514                                                                                
                                                                -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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: BRO1] (11)
(-)
Family: BRO1 (11)
(-)
Homo sapiens (Human) (10)
1aBRO1-2vsvB01B:514-517
1bBRO1-2vsvB02B:514-517

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RHPN2_HUMAN | Q8IUC4)
biological process
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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    Ala A:534 - Pro A:535   [ RasMol ]  
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