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(-) Description

Title :  CRYSTAL STRUCTURE OF MYO5B GLOBULAR TAIL DOMAIN IN COMPLEX WITH INACTIVE RAB11A
 
Authors :  O. Pylypenko, W. Attanda, C. Gauquelin, A. Houdusse
Date :  29 Jul 13  (Deposition) - 20 Nov 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dil, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pylypenko, W. Attanda, C. Gauquelin, M. Lahmani, D. Coulibaly, B. Baron, S. Hoos, M. A. Titus, P. England, A. M. Houdusse
Structural Basis Of Myosin V Rab Gtpase-Dependent Cargo Recognition.
Proc. Natl. Acad. Sci. Usa V. 110 20443 2013
PubMed-ID: 24248336  |  Reference-DOI: 10.1073/PNAS.1314329110

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-11A
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDILUTE DOMAIN RESIDUES 1456-1848
    GeneRAB11A, RAB11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB-11, YL8
 
Molecule 2 - UNCONVENTIONAL MYOSIN-VB
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-177
    GeneMYO5B, KIAA1119
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY 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 , SER A:40 , ASN A:124 , LYS A:125 , ASP A:127 , LEU A:128 , SER A:154 , ALA A:155 , LEU A:156 , MG A:202 , HOH A:302 , HOH A:307 , HOH A:308 , HOH A:317BINDING SITE FOR RESIDUE GDP A 201
2AC2SOFTWARESER A:25 , THR A:43 , GDP A:201 , HOH A:302 , HOH A:307 , HOH A:308BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASP C:19 , GLY C:21 , VAL C:22 , GLY C:23 , LYS C:24 , SER C:25 , ASN C:26 , PHE C:36 , ASN C:37 , LEU C:38 , SER C:40 , ASN C:124 , LYS C:125 , ASP C:127 , LEU C:128 , SER C:154 , ALA C:155 , LEU C:156 , MG C:202 , HOH C:301 , HOH C:315BINDING SITE FOR RESIDUE GDP C 201
4AC4SOFTWARESER C:25 , THR C:43 , GDP C:201 , HOH C:301 , HOH C:302BINDING SITE FOR RESIDUE MG C 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LWZ)

(-) 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:162
                                                                                                                                                                                                   
               SCOP domains d4lwza_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lwz A    7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTARAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIY  173
                                    16        26        36        46        56        66 ||     81        91       101       111       121       131       141       151       161       171  
                                                                                        68|                                                                                                   
                                                                                         74                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhhhhhh.........................hhhhh..hhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lwz B 1457 VTVQRKEKDFQGMLEYHKEDEALLIRNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHNDDFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQIYQQLIKIAEGVLQPMIVSAMLENESISYCLEAIIRQMNAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQLRYNISQLEEWLRGRNLHQSGAVQTMEPLIQAAQLLQLKKKTQEDAEAICSLCTSLSTQQIVKILNLYTPLFEERVTVAFIRTIQAQLQERNDPQQLLLDAKHMFPVLFPFNPSSLTMDSIHIPACLNLEFLNEV 1848
                                  1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626||    1659      1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779  ||  1791      1801      1811      1821      1831      1841       
                                                                                                                                                                                                   1627|                                                                                                                               1782|                                                               
                                                                                                                                                                                                    1651                                                                                                                                1785                                                               

Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                            
               SCOP domains d4lwzc_ C: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lwz C   10 YLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTATSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI  172
                                    19        29        39        49        59        77        87        97       107       117       127       137       147       157       167     
                                                                                     68|                                                                                               
                                                                                      77                                                                                               

Chain D from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhh...................hhhhh..hhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lwz D 1454 SMQVTVQRKEKDFQGMLEYHKEDEALLIRNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHNDDFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQIYQQLIKIAEGVLQPVSAMLENESYCLEAIIRQMNAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNDVCSWSTGMQLRYNISQLEEWLRGRNLHQSGAVQTMEPLIQAAQLLQLKTQEDAEAICSLCTSTQQIVKILNLYTPEERVTVAFIRTIQAQLQEDAKHMFPVLFPFNPSSLTMDSIHIPACLNLEFLNEV 1848
                                  1463      1473      1483      1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613 ||   1625||    1660      1670      1680      1690     |1705      1715      1725      1735      1745   || 1757      1769      1779 ||   1793      1803|     1822      1832      1842      
                                                                                                                                                                                          1615|    1626|                                        1696|                                           1749|         1765|         1781|             1803|                                   
                                                                                                                                                                                           1618     1652                                         1702                                            1752          1768          1786              1813                                   

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (66, 77)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYO5B_HUMAN | Q9ULV04j5m 4lnz 4lx0
        RB11A_HUMAN | P624911oiv 1oiw 1oix 1yzk 2d7c 2gzd 2gzh 2hv8 4c4p 4d0l 4d0m 4lx0 4uj3 4uj4 4uj5 5c46 5c4g 5euq 5ez5 5fbl 5fbq 5fbr 5fbv 5fbw 5jcz

(-) Related Entries Specified in the PDB File

4lx0 4lx1 4lx2