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(-) Description

Title :  STRUCTURE OF THE CGMP DEPENDENT PROTEIN KINASE II AND RAB11B COMPLEX
 
Authors :  A. S. Reger, M. P. Yang, E. Guo, C. Kim
Date :  21 Jan 14  (Deposition) - 06 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Small Gtpase, Leucine Zipper, Trafficking, Serine/Threonine Kinase, Membrane Associated, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. S. Reger, M. P. Yang, S. Koide-Yoshida, E. Guo, S. Mehta, K. Yuasa, A. Liu, D. E. Casteel, C. Kim
Crystal Structure Of The Cgmp-Dependent Protein Kinase Ii Leucine Zipper And Rab11B Protein Complex Reveals Molecular Details Of G-Kinase-Specific Interactions.
J. Biol. Chem. V. 289 25393 2014
PubMed-ID: 25070890  |  Reference-DOI: 10.1074/JBC.M114.575894

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-11B
    ChainsA, B
    EC Number3.6.5.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRAB11B, YPT3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGTP-BINDING PROTEIN YPT3
 
Molecule 2 - CGMP-DEPENDENT PROTEIN KINASE 2
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 40-83
    GenePRKG2
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymCGK 2, CGK2, CGMP-DEPENDENT PROTEIN KINASE II, CGKII

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A (1x)B (1x)C (1x)D (1x)
Biological Unit 2 (1x)A C 
Biological Unit 3 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , GLY A:21 , VAL A:22 , GLY A:23 , LYS A:24 , SER A:25 , ASN A:26 , PHE A:36 , ASN A:37 , LEU A:38 , GLU A:39 , LYS A:41 , ARG A:74 , ALA A:75 , ASN A:124 , LYS A:125 , ASP A:127 , LEU A:128 , SER A:154 , ALA A:155 , LEU A:156 , HOH A:401BINDING SITE FOR RESIDUE GDP A 301
2AC2SOFTWAREASP B:19 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , ASN B:26 , PHE B:36 , ASN B:37 , LEU B:38 , GLU B:39 , ASN B:124 , LYS B:125 , ASP B:127 , SER B:154 , ALA B:155 , LEU B:156BINDING SITE FOR RESIDUE GDP B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OJK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OJK)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhhhhhh.............eeeeeeee..eeeeeeeee......hhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ojk A   6 GSYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQK 179
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    

Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ojk B   7 SYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLEIGVEFATRSIQVDGKTIKAQIWDTITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQ 178
                                    16        26        36  ||    50        60      ||78        88        98       108       118       128       138       148       158       168       178
                                                           39|                     67|                                                                                                      
                                                            44                      76                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4ojk C  47 REYHLKELREQLAKQTVAIAELTEELQSKCIQLNKLQ  83
                                    56        66        76       

Chain D from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 4ojk D  49 YHLKELREQLAKQTVAIAELTEELQSKCIQLNK  81
                                    58        68        78   

   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4OJK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (52, 55)

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  RB11B_HUMAN | Q15907
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 Related Entries

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

UniProtKB/Swiss-Prot
        RB11B_HUMAN | Q159072f9l 2f9m

(-) Related Entries Specified in the PDB File

1zxa SOLUTION STRUCTURE OF THE COILED-COIL DOMAIN OF CGMP- DEPENDENT PROTEIN KINASE IA
2f9l 3D STRUCTURE OF INACTIVE HUMAN RAB11B GTPASE
2f9m 3D STRUCTURE OF ACTIVE HUMAN RAB11B GTPASE
3nmd CRYSTAL STRUCTURE OF THE LEUCINE ZIPPER DOMAIN OF CGMP DEPENDENT PROTEIN KINASE I BETA