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(-) Description

Title :  CRYSTAL STRUCTURE OF A CHIMERIC FUSION OF HUMAN DNAJ (HSP40) AND CAMP-DEPENDENT PROTEIN KINASE A (CATALYTIC ALPHA SUBUNIT)
 
Authors :  J. Cheung, C. Ginter, M. Cassidy, M. C. Franklin, M. J. Rudolph, W. A. Hen
Date :  02 Sep 14  (Deposition) - 21 Jan 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,I,J
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  B,J  (1x)
Keywords :  Chaperone, Catalysis, Protein Kinase, Adenosine Triphosphate, Phosphorylation, Chimera, Fusion, Fibrolamellar Hepatocellular Carinoma (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Cheung, C. Ginter, M. Cassidy, M. C. Franklin, M. J. Rudolph, N. Robine, R. B. Darnell, W. A. Hendrickson
Structural Insights Into Mis-Regulation Of Protein Kinase A In Human Tumors.
Proc. Natl. Acad. Sci. Usa V. 112 1374 2015
PubMed-ID: 25605907  |  Reference-DOI: 10.1073/PNAS.1424206112

(-) Compounds

Molecule 1 - DNAJ HOMOLOG SUBFAMILY B MEMBER 1,CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
    Chains: A, B
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLATE11
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP P25685 RESIDUES 2-70,UNP P17612 RESIDUES 16-351
    Gene: DNAJB1, DNAJ1, HDJ1, HSPF1, PRKACA, PKACA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNAJ PROTEIN HOMOLOG 1,HEAT SHOCK 40 KDA PROTEIN 1,HEAT SHOCK PROTEIN 40,HUMAN DNAJ PROTEIN 1,HDJ-1,PKA C-ALPHA
 
Molecule 2 - PKI (5-24)
    Chains: I, J
    Engineered: YES
    Fragment: RESIDUES 5-24
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABIJ
Biological Unit 1 (1x): A I 
Biological Unit 2 (1x):  B J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric Unit (4, 23)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2SEP4Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
4ZN15Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2SEP2Mod. Amino AcidPHOSPHOSERINE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2SEP2Mod. Amino AcidPHOSPHOSERINE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:105 , GLY A:107 , SER A:108 , PHE A:109 , GLY A:110 , VAL A:112 , ALA A:125 , LYS A:127 , VAL A:159 , MET A:175 , GLU A:176 , VAL A:178 , GLU A:182 , ASP A:221 , LYS A:223 , GLU A:225 , ASN A:226 , LEU A:228 , THR A:238 , ASP A:239 , PHE A:382 , ZN A:502 , ZN A:503 , HOH A:706 , HOH A:734 , HOH A:735 , HOH A:819 , ARG I:18 , ASN I:20 , ALA I:21binding site for residue ATP A 501
02AC2SOFTWAREASN A:226 , ASP A:239 , ATP A:501 , HOH A:706binding site for residue ZN A 502
03AC3SOFTWAREASP A:239 , ATP A:501 , HOH A:734 , HOH A:735binding site for residue ZN A 503
04AC4SOFTWAREGLU A:79 , ASP A:80 , HOH A:606 , HIS B:94 , ASP B:96binding site for residue ZN A 504
05AC5SOFTWARESEP A:194 , HIS A:197 , HOH A:1065 , HOH J:209binding site for residue ZN A 505
06AC6SOFTWAREGLU A:176 , GLN A:236 , HOH A:905 , HOH A:912binding site for residue ZN A 506
07AC7SOFTWAREHIS A:123 , HOH A:916 , HOH A:1010binding site for residue ZN A 507
08AC8SOFTWAREGLY B:105 , GLY B:107 , SER B:108 , PHE B:109 , GLY B:110 , VAL B:112 , ALA B:125 , LYS B:127 , VAL B:159 , MET B:175 , GLU B:176 , VAL B:178 , GLU B:182 , ASP B:221 , LYS B:223 , GLU B:225 , ASN B:226 , LEU B:228 , THR B:238 , ASP B:239 , PHE B:382 , ZN B:502 , ZN B:503 , HOH B:720 , HOH B:774 , HOH B:775 , HOH B:906 , ARG J:18 , ASN J:20 , ALA J:21binding site for residue ATP B 501
09AC9SOFTWAREASN B:226 , ASP B:239 , ATP B:501 , HOH B:906binding site for residue ZN B 502
10AD1SOFTWAREASP B:239 , ATP B:501 , HOH B:774 , HOH B:775binding site for residue ZN B 503
11AD2SOFTWAREHIS A:94 , ASP A:96 , GLU B:79 , ASP B:80 , HOH B:603binding site for residue ZN B 504
12AD3SOFTWARESEP B:194 , HIS B:197 , HOH B:633 , HOH B:848binding site for residue ZN B 505
13AD4SOFTWAREHIS I:23 , ZN I:102 , ZN I:103 , ZN J:101 , ZN J:102binding site for residue ZN I 101
14AD5SOFTWAREZN I:101 , ZN J:101binding site for residue ZN I 102
15AD6SOFTWAREHIS I:23 , ZN I:101 , HIS J:23 , ZN J:101binding site for residue ZN I 103
16AD7SOFTWAREZN I:101 , ZN I:102 , ZN I:103 , HIS J:23 , ZN J:102binding site for residue ZN J 101
17AD8SOFTWAREZN I:101 , ZN J:101binding site for residue ZN J 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WB7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WB7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WB7)

(-) Exons   (0, 0)

(no "Exon" information available for 4WB7)

(-) 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:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.......hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wb7 A   1 GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFsEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFSEF 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   |   200       210       220       230       240       250 |     260       270       280       290       300       310       320       330       340       350       360       370       380       390  |    400     
                                                                                                                                                                                                                           194-SEP                                                   252-TPO                                                                                                                                      393-SEP        


Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.......hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wb7 B   1 GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFsEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFSEF 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   |   200       210       220       230       240       250 |     260       270       280       290       300       310       320       330       340       350       360       370       380       390  |    400     
                                                                                                                                                                                                                           194-SEP                                                   252-TPO                                                                                                                                      393-SEP        


Chain I from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4wb7 I   5 TTYADFIASGRTGRRNAIHD  24
                                    14        24


Chain J from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4wb7 J   5 TTYADFIASGRTGRRNAIHD  24
                                    14        24
   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 4WB7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WB7)

(-) Gene Ontology  (99, 108)

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  4wb7
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  DNJB1_HUMAN | P25685
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  IPKA_HUMAN | P61925
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  KAPCA_HUMAN | P17612
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  2.7.11.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNJB1_HUMAN | P25685: 1hdj 2qld 3agx 3agy 3agz
        IPKA_HUMAN | P61925: 1cdk 1cmk 1ctp 1jlu 1q24 1q61 1q62 1q8t 1q8u 1q8w 1smh 1stc 1sve 1svg 1svh 1veb 1xh4 1xh5 1xh6 1xh7 1xh8 1xh9 1xha 1ydr 1yds 1ydt 2c1a 2c1b 2f7e 2gni 2jds 2jdt 2jdv 2l1l 2uvx 2uvy 2uvz 2uw0 2uw3 2uw4 2uw5 2uw6 2uw7 2uw8 2vnw 2vny 2vo0 2vo3 2vo6 2vo7 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 3wyg 3x2u 3x2v 3x2w 4axa 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib1 4ib3 4ie9 4ij9 4o21 4o22 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb8 4z83 4z84 5bx6 5bx7 5dh9
        KAPCA_HUMAN | P17612: 2gu8 3agl 3agm 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 4ae6 4ae9 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb8 5bx6 5bx7 5izf 5izj 5j5x

(-) Related Entries Specified in the PDB File

4wb5 4wb6 4wb8