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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE RPGR RCC1-LIKE DOMAIN IN COMPLEX WITH PDE6D
 
Authors :  D. Waetzlich, I. Vetter, A. Wittinghofer, S. Ismail
Date :  05 Mar 13  (Deposition) - 17 Apr 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Immunoglobulin-Like Beta-Sandwich, Rcc1-Like Domain, Beta Propellar, Seven Bladed-Propeller, Structural Protein, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Watzlich, I. Vetter, K. Gotthardt, M. Miertzschke, Y. X. Chen, A. Wittinghofer, S. Ismail
The Interplay Between Rpgr, Pde-Delta And Arl2/3 Regulate The Ciliary Targeting Of Farnesylated Cargo.
Embo Rep. V. 14 465 2013
PubMed-ID: 23559067  |  Reference-DOI: 10.1038/EMBOR.2013.37

(-) Compounds

Molecule 1 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePDE6D, PDED
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGMP-PDE DELTA, PROTEIN P17
 
Molecule 2 - X-LINKED RETINITIS PIGMENTOSA GTPASE REGULATOR
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRPGR (8-368) THE RCC1-LIKE DOMAIN
    GeneRPGR, RP3, XLRP3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4JHP)

(-) Sites  (0, 0)

(no "Site" information available for 4JHP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JHP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu C:24 -Asn C:25
2Asn C:25 -Asn C:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JHP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JHP)

(-) Exons   (0, 0)

(no "Exon" information available for 4JHP)

(-) 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 B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains d4jhpb_ B: GMP-PDE delta                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee...hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jhp B   4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    13        23        33        43        53        63        73        83        93       103       118       128       138       148  
                                                                                                                                     111|                                 
                                                                                                                                      117                                 

Chain C from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..........ee......eeeeee...eeeeee....eeeee..................ee.hhhh...eeeeee...eeeeee....eeeee..............eeeeee.........eeeeee...eeeeee....eeeeee............eeeeeeee.....eeeeee...eeeeee....eeeee.........hhhhhhhh...ee.......eeeeee...eeeeee...eeeeee.............eeeeeee.hhhh...eeeeee...eeeeee....eeeee.hhhhh..........eeeeee.hhhh.eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jhp C   7 LMPDSGAVFTFGKSKFAENNPGKFWFKNDVPVHLSCGDEHSAVVTGNNKLYMFGSNNWGQLGLGSKSAISKPTCVKALKPEKVKLAACGRNHTLVSTEGGNVYATGGNNEGQLGLGDTEERNTFHVISFFTSEHKIKQLSAGSNTSAALTEDGRLFMWGDNSEGQIGLKNVSNVCVPQQVTIGKPVSWISCGYYHSAFVTTDGELYVFGEPENGKLGLPNQLLGNHRTPQLVSEIPEKVIQVACGGEHTVVLTENAVYTFGLGQFGQLGLGTFLFETSEPKVIENIRDQTISYISCGENHTALITDIGLMYTFGDGRHGKLGLGLENFTNHFIPTLCSNFLRFIVKLVACGGCHMVVFAAPH 368
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  

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    → 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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JHP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JHP)

(-) Gene Ontology  (26, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Sites" information available for 4jhp)
 
  Cis Peptide Bonds
    Asn C:25 - Asn C:26   [ RasMol ]  
    Glu C:24 - Asn C:25   [ RasMol ]  
 

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  RPGR_HUMAN | Q92834
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE6D_HUMAN | O439241ksg 1ksh 1ksj 3t5g 3t5i 4jv6 4jv8 4jvb 4jvf 5e80 5e8f 5f2u 5ml2 5ml3 5ml4 5ml6 5ml8 5nal 5tar 5tb5
        RPGR_HUMAN | Q928344jhn 4qam

(-) Related Entries Specified in the PDB File

4jhn