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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRANSITION STATE MIMIC OF THE GSK-3/AXIN COMPLEX BOUND TO PHOSPHORYLATED N-TERMINAL AUTO-INHIBITORY PS9 PEPTIDE
 
Authors :  M. L. -H. Chu, J. L. Stamos, M. D. Enos, N. Shah, W. I. Weis
Date :  03 Dec 13  (Deposition) - 26 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wnt, Lrp6, Gsk-3, Axin, Kinase, Primed Substrate, Transition State, Phosphorylated N-Terminal Auto-Inhibitory Ps9 Peptide, Transferase- Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Stamos, M. L. Chu, M. D. Enos, N. Shah, W. I. Weis
Structural Basis Of Gsk-3 Inhibition By N-Terminal Phosphorylation And By The Wnt Receptor Lrp6.
Elife V. 3 01998 2014
PubMed-ID: 24642411

(-) Compounds

Molecule 1 - GLYCOGEN SYNTHASE KINASE-3 BETA
    Chains: A
    EC Number: 2.7.11.26, 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B(+)
    Expression System Strain: BL21(DE3)CODON-PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-383 WITH PHOSPHOYLATED SER9
    Gene: GSK3B
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GSK-3 BETA, SERINE/THREONINE-PROTEIN KINASE GSK3B
 
Molecule 2 - AXIN-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PGEX-KG
    Expression System Strain: BL21(DE3)CODON-PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 383-402
    Gene: AXIN1, AXIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AXIS INHIBITION PROTEIN 1, HAXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3GOL2Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NO31Ligand/IonNITRATE ION
6SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:26 , TYR A:56 , TYR A:71 , LYS A:86 , SER A:118 , ASN A:129BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREARG A:144 , SER A:147 , GLN A:254 , PRO A:255 , ILE A:256BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREASN A:186 , ASP A:200 , ADP A:405 , AF3 A:406 , HOH A:576BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREASP A:181 , ASP A:200 , ADP A:405 , AF3 A:406 , HOH A:507 , HOH A:562BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWAREGLY A:65 , SER A:66 , PHE A:67 , GLY A:68 , VAL A:70 , ALA A:83 , LYS A:85 , ASP A:133 , TYR A:134 , VAL A:135 , THR A:138 , ARG A:141 , GLN A:185 , ASN A:186 , LEU A:188 , ASP A:200 , MG A:403 , MG A:404 , AF3 A:406 , HOH A:512 , HOH A:562 , HOH A:576BINDING SITE FOR RESIDUE ADP A 405
6AC6SOFTWAREGLY A:65 , SER A:66 , PHE A:67 , ASP A:181 , LYS A:183 , ASN A:186 , ASP A:200 , MG A:403 , MG A:404 , ADP A:405BINDING SITE FOR RESIDUE AF3 A 406
7AC7SOFTWAREASP A:49 , PRO A:51 , TYR A:146 , TYR A:157 , TYR A:161BINDING SITE FOR RESIDUE NO3 A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NU1)

(-) Exons   (0, 0)

(no "Exon" information available for 4NU1)

(-) 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....eeeeeee.......eeeeeeeeeeee....eeeeeeee.....eeeeeeee.......hhhhhhh.........eeeeeee......eeeeeee...eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eeee....eeee......ee.................hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nu1 A   6 RTTsFAMKVSSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR 383
                               | || 29|       44        54        64        74        84        94       104       114    || 126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       
                               | || 29|                                                                                 119|                                                                                                                                                                                                                                                                     
                               9-SEP 35                                                                                  122                                                                                                                                                                                                                                                                     
                                11|                                                                                                                                                                                                                                                                                                                                                              
                                 26                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4nu1 B 383 VEPQKFAEELIHRLEAVQR 401
                                   392
   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 4NU1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NU1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NU1)

(-) Gene Ontology  (189, 207)

Asymmetric/Biological Unit(hide GO term definitions)

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  GSK3B_MOUSE | Q9WV60
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 Related Entries

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

UniProtKB/Swiss-Prot
        AXIN1_HUMAN | O15169: 1dk8 1emu 1o9u 3zdi 4b7t 4nm0 4nm3 4nm5 4nm7
        GSK3B_MOUSE | Q9WV60: 5air

(-) Related Entries Specified in the PDB File

4nm0 THE SAME PROTEIN IS A PEPTIDE INHIBITOR-FREE GSK-3/AXIN COMPLEX
4nm3 THE SAME PROTEIN COMPLEXED WITH ITS OWN PHOSPHORYLATED N- TERMINAL AUTO-INHIBITORY PS9 PEPTIDE BUT WITHOUT ALF3
4nm5 THE SAME PROTEIN COMPLEXED WITH PHOSPHORYLATED WNT RECEPTOR LRP6 C-MOTIF
4nm7 THE SAME PROTEIN COMPLEXED WITH PHOSPHORYLATED WNT RECEPTOR LRP6 E-MOTIF