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(-) Description

Title :  CRYSTAL STRUCTURE OF JNK IN COMPLEX WITH A REGULATOR PROTEIN
 
Authors :  X. Liu, J. Wang, J. W. Wu, Z. X. Wang
Date :  14 Mar 15  (Deposition) - 16 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  E,G  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  F,H  (1x)
Keywords :  Kinase Domain, Catalytic Domain, Transferase-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Liu, C. S. Zhang, C. Lu, S. C. Lin, J. W. Wu, Z. X. Wang
A Conserved Motif In Jnk/P38-Specific Mapk Phosphatases As Determinant For Jnk1 Recognition And Inactivation.
Nat Commun V. 7 10879 2016
PubMed-ID: 26988444  |  Reference-DOI: 10.1038/NCOMMS10879

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 8
    Chains: E, A, C, F
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-363
    Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAPK 8,JNK-46,STRESS-ACTIVATED PROTEIN KINASE 1C,SAPK1C, STRESS-ACTIVATED PROTEIN KINASE JNK1,C-JUN N-TERMINAL KINASE 1
 
Molecule 2 - DUAL SPECIFICITY PROTEIN PHOSPHATASE 16
    Chains: G, B, D, H
    EC Number: 3.1.3.16, 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 156-301
    Gene: DUSP16, KIAA1700, MKP7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 7,MKP-7

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):     E G 
Biological Unit 2 (1x): AB      
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):      F H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS G:244 , HOH G:507binding site for residue CL G 401
2AC2SOFTWAREARG B:250binding site for residue CL B 401
3AC3SOFTWARECYS D:244 , ARG D:250binding site for residue CL D 401
4AC4SOFTWARECYS H:244 , ARG H:250binding site for residue CL H 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YR8)

(-) Exons   (0, 0)

(no "Exon" information available for 4YR8)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee..eeeeee...eeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee..........eeeeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee............hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhh...hhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 A   8 NNFYSVEIGDSTFTVLKRYQNLKPIGGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLAVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAIEEWKELIYKEVMD 362
                                    17        27     || 41        51        61        71        81        91       101       111       121       131       141       151       161       171 ||    194       204       214       224       234       244       254       264       274       284       294       304       314       324     ||352       362
                                                    33|                                                                                                                                    173|                                                                                                                                            330|             
                                                     38                                                                                                                                     187                                                                                                                                             349             


Chain B from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeehhhhhhhhhhhhh...eeee...........hhh.eee..........hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 B 158 GPTRILPNLYLGCQRDVLNKELMQQNGIGYVLNASNTCPKPDFIPESHFLRVPVNDSFCEKILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATIAIAYIMKRMDMSLDEAYRFVKEKRPTISPNFNFLGQLLDYEKKI 298
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297 


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeee...eeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee...........eeeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yr8 C  10 FYSVDSTFTVLKRYQNLKPIGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDEWKELIYKEVMD 362
                               ||   22        32||      47        57        67        77        87        97       107       117       127       137       147       157       167   ||  193       203       213       223       233       243       253       263       273       283       293       303       313       323       333     ||354        
                              13|              33|                                                                                                                                 171|                                                                                                                                                    339|           
                               17               39                                                                                                                                  188                                                                                                                                                     351           


Chain D from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeehhhhhhhhhhhhhh.eeeeee...........hhh.eee..........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 D 158 GPTRILPNLYLGCQRDVLNKELMQQNGIGYVLNASNTCPKPDFIPESHFLRVPVNDSFCEKILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATIAIAYIMKRMDMSLDEAYRFVKEKRPTISPNFNFLGQLLDYEKKIK 299
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297  


Chain E from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeeee..eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee..........eeeeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.............hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhh...hhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 E   7 DNNFYSVEIGDSTFTVLKRYQNLKPIGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAKELIYKEVMD 362
                                    16        26     || 41        51        61        71        81        91       101       111       121       131       141       151       161       171  ||   193       203       213       223       233       243       253       263       273       283       293       303       313       323      |355       
                                                    32|                                                                                                                                     174|                                                                                                                                            330|         
                                                     38                                                                                                                                      187                                                                                                                                             353         


Chain F from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....eee.....eeeee....eeeee...eeeee......hhhhhhhhhhhhhhhh.......eeeee..eeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhhh........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yr8 F  10 FYSVEIGDSTFTVLKRYQNLKPIGGIVCAAYDRNVAIKKLPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPELIYKEVMD 362
                                    19        29   ||   43 ||     57|       69        79        89   ||  109       119       129       139       149       159       169 ||    195       205       215       225       235       245       255       265       275       287       297       307       317       327       337||     362
                                                  33|     45|     57|                               93|                                                                171|                                                                                            283|                                                 338|        
                                                   38      50      60                               104                                                                 188                                                                                             286                                                  354        


Chain G from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeehhhhhhhhhhhhhh..eeee...........hhh.eee.............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 G 158 GPTRILPNLYLGCQRDVLNKELMQQNGIGYVLNASNTCPKPDFIPESHFLRVPVNDSFCEKILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATIAIAYIMKRMDMSLDEAYRFVKEKRPTISPNFNFLGQLLDYEKKI 298
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297 


Chain H from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeehhhhhhhhhhhhhh.eeeeee...........hhh.eee..........hhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr8 H 158 GPTRILPNLYLGCQRDVLNKELMQQNGIGYVLNASNTCPKPDFIPESHFLRVPVNDSFCEKILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATIAIAYIMKRMDMSLDEAYRFVKEKRPTISPNFNFLGQLLDYEKKIKN 300
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297
   Legend:   → Mismatch (orange background)
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    → 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 4YR8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YR8)

(-) Gene Ontology  (56, 60)

Asymmetric Unit(hide GO term definitions)

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  4yr8
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  MK08_HUMAN | P45983
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 Related Entries

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

UniProtKB/Swiss-Prot
        DUS16_HUMAN | Q9BY84: 2vsw 3tg3
        MK08_HUMAN | P45983: 1ukh 1uki 2g01 2gmx 2h96 2no3 2xrw 2xs0 3elj 3o17 3o2m 3pze 3v3v 3vud 3vug 3vuh 3vui 3vuk 3vul 3vum 4awi 4e73 4g1w 4hys 4hyu 4izy 4l7f 4qtd 4ux9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YR8)