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(-) Description

Title :  CRYSTAL STRUCTURE OF GSK-3/AXIN COMPLEX BOUND TO PHOSPHORYLATED WNT RECEPTOR LRP6 C-MOTIF
 
Authors :  J. L. Stamos, M. L. -H. Chu, M. D. Enos, N. Shah, W. I. Weis
Date :  14 Nov 13  (Deposition) - 26 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Wnt, Lrp6, Auto-Inhibited, Gsk-3, Axin, Kinase, Primed Substrate, Phosphorylated Wnt Receptor Lrp6 C-Motif, 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 - GSK3B PROTEIN
    Chains: A
    EC Number: 2.7.11.26
    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 13-383
    Gene: GSK3B, HCG_1818062
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GSK3BETA ISOFORM, GLYCOGEN SYNTHASE KINASE 3 BETA, ISOFORM CRA_B, CDNA FLJ75266, HIGHLY SIMILAR TO HOMO SAPIENS GLYCOGEN SYNTHASE KINASE 3 BETA, MRNA
 
Molecule 2 - AXIN-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    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
 
Molecule 3 - PHOSPHORYLATED WNT RECEPTOR LRP6 C-MOTIF
    Chains: C
    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 1568-1575
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:67 , ALA A:83 , LYS A:85 , VAL A:110 , LEU A:132 , ASP A:133 , TYR A:134 , VAL A:135 , THR A:138 , ARG A:141 , GLN A:185 , ASN A:186 , ASP A:200 , MG A:406 , MG A:407 , HOH A:554 , HOH A:572BINDING SITE FOR RESIDUE ADP A 401
2AC2SOFTWARETYR A:56 , LYS A:86 , SER A:118 , ASN A:129BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREARG A:144 , ARG A:148 , LYS A:150 , LEU A:252 , GLN A:254 , PRO A:255BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREARG A:319 , THR A:326 , ALA A:327 , ARG A:328 , THR A:330 , GLU A:333BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWARELYS A:271 , HIS A:299BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREASN A:186 , ASP A:200 , ADP A:401 , HOH A:572BINDING SITE FOR RESIDUE MG A 406
7AC7SOFTWAREASP A:200 , GLY A:202 , ADP A:401 , HOH A:537BINDING SITE FOR RESIDUE MG A 407
8AC8SOFTWAREILE A:296 , LYS A:297BINDING SITE FOR RESIDUE CL A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NM5)

(-) Exons   (0, 0)

(no "Exon" information available for 4NM5)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4nm5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeeeeee.......eeeeeeeeeeeee...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
                4nm5 A   24 GSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARH  384
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 


Chain B from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                4nm5 B  383 VEPQKFAEELIHRLEAVQR  401
                                   392         


Chain C from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                4nm5 C 1569 PPPtPR 1574
                               |  
                            1572-TPO
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NM5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NM5)

(-) Gene Ontology  (254, 303)

Asymmetric Unit(hide GO term definitions)

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  4nm5
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  LRP6_HUMAN | O75581
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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 4nm7 4nu1
        GSK3B_HUMAN | P49841: 1gng 1h8f 1i09 1j1b 1j1c 1o6k 1o6l 1o9u 1pyx 1q3d 1q3w 1q41 1q4l 1q5k 1r0e 1uv5 2jdo 2jdr 2jld 2o5k 2ow3 2uw9 2x39 2xh5 3cqu 3cqw 3du8 3e87 3e88 3e8d 3f7z 3f88 3gb2 3i4b 3l1s 3m1s 3mv5 3ow4 3pup 3q3b 3qkk 3say 3sd0 3zdi 3zrk 3zrl 3zrm 4acc 4acd 4acg 4ach 4afj 4b7t 4dit 4ekk 4iq6 4j1r 4j71 4nm0 4nm3 4nm7 4ptc 4pte 4ptg 5f94 5f95 5hln 5hlp 5k5n
        LRP6_HUMAN | O75581: 3s2k 3s8v 3s8z 3s94 3sob 3soq 3sov 4a0p 4dg6 4nm7 5air 5fww 5gje
        Q6FI27_HUMAN | Q6FI27: 4nm7

(-) 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
4nm7 THE SAME PROTEIN COMPLEXED WITH PHOSPHORYLATED WNT RECEPTOR LRP6 C-MOTIF
4nu1 THE SAME PROTEIN COMPLEXED WITH ITS OWN PHOSPHORYLATED N- TERMINAL AUTO-INHIBITORY PS9 PEPTIDE AND ALF3 IS A TRANSITION STATE MIMICRY