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(-) Description

Title :  STRUCTURE OF HUMAN RAB10 IN COMPLEX WITH THE BMERB DOMAIN OF MICAL-1
 
Authors :  A. Rai, A. Oprisko, J. Campos, Y. Fu, T. Friese, A. Itzen, R. S. Goody, M. P E. M. Gazdag
Date :  14 Aug 16  (Deposition) - 24 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Mical-1, Duf3585, Mical, Rab Effector, Rab10, Oxidoreductase, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Rai, A. Oprisko, J. Campos, Y. Fu, T. Friese, A. Itzen, R. S. Goody, E. M. Gazdag, M. P. Muller
Bmerb Domains Are Bivalent Rab8 Family Effectors Evolved By Gene Duplication.
Elife V. 5 2016
PubMed-ID: 27552051  |  Reference-DOI: 10.7554/ELIFE.18675

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-10
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRAB10
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - PROTEIN-METHIONINE SULFOXIDE OXIDASE MICAL1
    ChainsB
    EC Number1.14.13.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 918-1067
    GeneMICAL1, MICAL, NICAL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMOLECULE INTERACTING WITH CASL PROTEIN 1,MICAL-1,NEDD9- INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:23 , THR A:41 , ASP A:64 , GNP A:202 , HOH A:301 , HOH A:302binding site for residue MG A 201
2AC2SOFTWAREASP A:17 , SER A:18 , GLY A:19 , VAL A:20 , GLY A:21 , LYS A:22 , THR A:23 , CYS A:24 , PHE A:34 , ASN A:35 , THR A:36 , PHE A:38 , SER A:40 , THR A:41 , GLY A:67 , ASN A:122 , LYS A:123 , ASP A:125 , MET A:126 , SER A:152 , ALA A:153 , LYS A:154 , MG A:201 , HOH A:301 , HOH A:302binding site for residue GNP A 202
3AC3SOFTWARETHR C:23 , THR C:41 , GNP C:202 , HOH C:301 , HOH C:302binding site for residue MG C 201
4AC4SOFTWAREASP C:17 , SER C:18 , GLY C:19 , VAL C:20 , GLY C:21 , LYS C:22 , THR C:23 , CYS C:24 , PHE C:34 , ASN C:35 , THR C:36 , PHE C:38 , THR C:41 , GLY C:67 , ASN C:122 , LYS C:123 , ASP C:125 , MET C:126 , SER C:152 , ALA C:153 , LYS C:154 , MG C:201 , HOH C:301 , HOH C:302binding site for residue GNP C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LPN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LPN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LPN)

(-) Exons   (0, 0)

(no "Exon" information available for 5LPN)

(-) 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:171
                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lpn A    5 TYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKIKLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERMLLGNKCDMDDKRVVPKGKGEQIAREHGIRFFETSAKANINIEKAFLTLAEDILRKTP  175
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 

Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5lpn B  918 KEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQSSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYDRQAEDQVLRKLVDLVNQRDALIRFQEERRLSELA 1060
                                   927       937       947       957       967       977       987       997      1007      1028      1038      1048      1058  
                                                                                                                         1014|                                  
                                                                                                                          1026                                  

Chain C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeehhhhh.eeeeeeee..hhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhh......eeeee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lpn C    6 YDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKIKLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERMLLGNKCDMDDKRVVPKGKGEQIAREHGIETSAKANINIEKAFLTLAEDILRKTP  175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145||     158       168       
                                                                                                                                                                      146|                         
                                                                                                                                                                       150                         

   Legend:   → Mismatch (orange background)
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  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 5LPN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LPN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LPN)

(-) Gene Ontology  (67, 68)

Asymmetric/Biological Unit(hide GO term definitions)

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  RAB10_HUMAN | P61026
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 Related Entries

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

UniProtKB/Swiss-Prot
        MICA1_HUMAN | Q8TDZ21wyl 2co8 2dk9 5le0
        RAB10_HUMAN | P610265szj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LPN)