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(-) Description

Title :  STRUCTURE OF THE SNX17 FERM DOMAIN BOUND TO THE SECOND NPXF MOTIF OF KRIT1
 
Authors :  A. L. Stiegler, R. Zhang, W. Liu, T. J. Boggon
Date :  27 May 14  (Deposition) - 30 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Ferm Domain, Npxy Motif, Npxf Motif, Protein Transport-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Stiegler, R. Zhang, W. Liu, T. J. Boggon
Structural Determinants For Binding Of Sorting Nexin 17 (Snx17) To The Cytoplasmic Adaptor Protein Krev Interaction Trapped 1 (Krit1).
J. Biol. Chem. V. 289 25362 2014
PubMed-ID: 25059659  |  Reference-DOI: 10.1074/JBC.M114.584011

(-) Compounds

Molecule 1 - SORTING NEXIN-17
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SNX17, KIAA0064
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - KREV INTERACTION TRAPPED PROTEIN 1
    Chains: D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 225-237
    Gene: KRIT1, CCM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: KREV INTERACTION TRAPPED 1,CEREBRAL CAVERNOUS MALFORMATIONS 1 PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4TKN)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:320 -E:228

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:281 -Pro A:282
2Phe C:281 -Pro C:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TKN)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeee...hhhhhhhhhhhhhh.hhhhhh.eeeeeeee.....eeeeee.....hhhhhhhh.....eeeeeee...hhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhh.......ee...eee......eeeeeeee..eeeee....eeeee...eeeeeeee.....eeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tkn A 113 PTEEVSLEVLLSNGQKVLVNVLTSDQTEDVLEAVAAKLDLPDDLIGYFSLFLVREKEDGAFSFVRKLQEFELPYVSVTSLRSQEYKIVLRKSYWDSAYDDDVMENRVGLNLLYAQTVSDIERGWILVTKEQHRQLKSLQEKVSKKEFLRLAQTLRHYGYLRFDACVADFPEKDCPVVVSAGNSELSLQLRLREGSFRVTRMRCWRVTSSVPVRLELAFEYLMSKDRLQWVTITSPQAIMMSICLQSMVDELMVKKS 388
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302|      317       327||     352       362       372       382      
                                                                                                                                                                                                                       302|                 328|                                            
                                                                                                                                                                                                                        308                  344                                            


Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeee...hhhhhhhhhhhhhh.hhhhhh.eeeeeeee.....eeeeee.....hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhh.......ee....ee..eeeee..eeeee..eeee...eeeeeeee......eeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tkn B 113 PTEEVSLEVLLSNGQKVLVNVLTSDQTEDVLEAVAAKLDLPDDLIGYFSLFLVREKEDGAFSFVRKLQEFELPYVSVTSLRSQEYKIVLRKSYWDSAYDDDVMENRVGLNLLYAQTVSDIERGWILVTKEQHRQLKSLQEKVSKKEFLRLAQTLRHYGYLRFDACVADVVVSAGNSELSLQLEGSFRVTRMRCWRVTSSVPLVRLELAFEYLMSKDRLQWVTITSPQAIMMSICLQSMVDELMVKKS 388
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       289       299 ||    317       327 ||    351       361       371       381       
                                                                                                                                                                                                 280|          301|                329|                                            
                                                                                                                                                                                                  288           310                 344                                            


Chain C from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeee...hhhhhhhhhhhhhh.hhhhhh.eeeeeeee.....eeeeee.....hhhhhhhh.....eeeeeee...hhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhh.......ee...eee......eeeeeeee..eeeee....eeeee...eeeeeeee......eeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tkn C 113 PTEEVSLEVLLSNGQKVLVNVLTSDQTEDVLEAVAAKLDLPDDLIGYFSLFLVREKEDGAFSFVRKLQEFELPYVSVTSLRSQEYKIVLRKSYWDSAYDDDVMENRVGLNLLYAQTVSDIERGWILVTKEQHRQLKSLQEKVSKKEFLRLAQTLRHYGYLRFDACVADFPEKDCPVVVSAGNSELSLQLQLREGSFRVTRMRCWRVTSSVPLVRLELAFEYLMSKDRLQWVTITSPQAIMMSICLQSMVDELMVKKS 388
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       307       317       327 ||    351       361       371       381       
                                                                                                                                                                                                                      301|                   329|                                            
                                                                                                                                                                                                                       307                    344                                            


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..ee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4tkn D 227 TCIYNPLFGS 236
                                   236


Chain E from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..ee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4tkn E 227 TCIYNPLFG 235


Chain F from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..ee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4tkn F 227 TCIYNPLFG 235
   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 4TKN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 53)

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  Cis Peptide Bonds
    Phe A:281 - Pro A:282   [ RasMol ]  
    Phe C:281 - Pro C:282   [ RasMol ]  
 
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  4tkn
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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  KRIT1_HUMAN | O00522
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  SNX17_HUMAN | Q15036
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 Related Entries

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

UniProtKB/Swiss-Prot
        KRIT1_HUMAN | O00522: 3u7d 4dx8 4dxa 4hdo 4hdq 4jif 5d68
        SNX17_HUMAN | Q15036: 3fog 3lui 4gxb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4TKN)