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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED CONSTRUCT OF PHOSPHATIDYLINOSITOL 4 KINASE III BETA IN COMPLEX WITH GTP GAMMA S LOADED RAB11
 
Authors :  J. E. Burke, M. L. Fowler
Date :  17 Jun 15  (Deposition) - 20 Jan 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  E,F
Keywords :  Protein-Protein Complex, Lipid Kinase, Gtpase Complex, Transferase- Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Fowler, J. A. Mcphail, M. L. Jenkins, G. R. Masson, F. U. Rutaganira, K. M. Shokat, R. L. Williams, J. E. Burke
Using Hydrogen Deuterium Exchange Mass Spectrometry To Engineer Optimized Constructs For Crystallization Of Protei Complexes: Case Study Of Pi4Kiii Beta With Rab11.
Protein Sci. V. 25 826 2016
PubMed-ID: 26756197  |  Reference-DOI: 10.1002/PRO.2879

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4-KINASE BETA
    Chains: E
    EC Number: 2.7.1.67
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPTH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PI4KB, PIK4CB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS 4-KINASE BETA,NPIK
 
Molecule 2 - RAS-RELATED PROTEIN RAB-11A
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPTG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RAB11A, RAB11
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB-11,YL8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GSP1Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:605 , LYS E:608binding site for residue SO4 E 801
2AC2SOFTWARETYR E:183 , LYS E:195 , ARG E:232 , GLY E:233 , LYS E:235 , LEU E:236binding site for residue SO4 E 802
3AC3SOFTWAREGLY E:155 , SER F:20 , GLY F:21 , VAL F:22 , GLY F:23 , LYS F:24 , SER F:25 , ASN F:26 , PHE F:36 , ASN F:37 , LEU F:38 , SER F:40 , SER F:42 , THR F:43 , GLY F:69 , ASN F:124 , LYS F:125 , ASP F:127 , LEU F:128 , SER F:154 , ALA F:155 , LEU F:156 , MG F:2001binding site for residue GSP F 2000
4AC4SOFTWARESER F:25 , THR F:43 , GSP F:2000binding site for residue MG F 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C46)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu E:348 -Pro E:349

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C46)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C46)

(-) Exons   (0, 0)

(no "Exon" information available for 5C46)

(-) 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 E from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhee........eeeeeeeee.......................hhhhhhhhhhhh........eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..........eee.....eee.....eeehhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee................hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c46 E 128 SWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSRGTKLRKLILSDRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSM 782
                                   137       147       157       167       177       187       197       207       217   ||  237     ||309       319       329       339       349       359       369       379       389       399    || 516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676      |693       703       713       723       733       743       753       763       773         
                                                                                                                       221|        243|                                                                                               404|                                                                                                                                                                        683|                                                                                           
                                                                                                                        232         306                                                                                                512                                                                                                                                                                         691                                                                                           


Chain F from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhh............eeeeeeeeee..eeeeeeeeee..hhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c46 F   6 DEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQ 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
   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  (0, 0)

(no "SCOP Domain" information available for 5C46)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C46)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C46)

(-) Gene Ontology  (73, 82)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu E:348 - Pro E:349   [ RasMol ]  
 

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  5c46
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  RB11A_HUMAN | P62491
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  2.7.1.67
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 Related Entries

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

UniProtKB/Swiss-Prot
        PI4KB_HUMAN | Q9UBF8: 2n73 4d0l 4d0m 4wae 4wag 5c4g 5euq 5fbl 5fbq 5fbr 5fbv 5fbw 5lx2 5nas
        RB11A_HUMAN | P62491: 1oiv 1oiw 1oix 1yzk 2d7c 2gzd 2gzh 2hv8 4c4p 4d0l 4d0m 4lwz 4lx0 4uj3 4uj4 4uj5 5c4g 5euq 5ez5 5fbl 5fbq 5fbr 5fbv 5fbw 5jcz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5C46)