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(-) Description

Title :  CRYSTAL STRUCTURE OF PRMT5:MEP50 WITH EPZ015666 AND SINEFUNGIN
 
Authors :  P. A. Boriack-Sjodin
Date :  06 Dec 14  (Deposition) - 22 Apr 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Inhibitor Complex, Protein Arginine Methyltransferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Chan-Penebre, K. G. Kuplast, C. R. Majer, P. A. Boriack-Sjodin, T. J. Wigle, L. D. Johnston, N. Rioux, M. J. Munchhof, L. Jin, S. L. Jacques, K. A. West, T. Lingaraj, K. Stickland, S. A. Ribich, A. Raimondi, M. P. Scott, N. J. Waters, R. M. Pollock, J. J. Smith, O. Barbash, M. Pappalardi, T. F. Ho, K. Nurse, K. P. Oza, K. T. Gallagher R. Kruger, M. P. Moyer, R. A. Copeland, R. Chesworth, K. W. Duncan
A Selective Inhibitor Of Prmt5 With In Vivo And In Vitro Potency In Mcl Models.
Nat. Chem. Biol. V. 11 432 2015
PubMed-ID: 25915199  |  Reference-DOI: 10.1038/NCHEMBIO.1810

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 5
    ChainsA
    EC Number2.1.1.-, 2.1.1.125
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPDEST
    Expression System Vector TypeBACULOVIRUS
    GenePRMT5, HRMT1L5, IBP72, JBP1, SKB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym72 KDA ICLN-BINDING PROTEIN,HISTONE-ARGININE N- METHYLTRANSFERASE PRMT5,JAK-BINDING PROTEIN 1,SHK1 KINASE-BINDING PROTEIN 1 HOMOLOG,SKB1HS
 
Molecule 2 - METHYLOSOME PROTEIN 50
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPDEST
    Expression System Vector TypeBACULOVIRUS
    GeneWDR77, MEP50, WD45, HKMT1069, NBLA10071
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMEP-50,ANDROGEN RECEPTOR COFACTOR P44,WD REPEAT-CONTAINING PROTEIN 77,P44/MEP50

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
13XV1Ligand/IonN-[(2S)-3-(3,4-DIHYDROISOQUINOLIN-2(1H)-YL)-2-HYDROXYPROPYL]-6-(OXETAN-3-YLAMINO)PYRIMIDINE-4-CARBOXAMIDE
2GOL3Ligand/IonGLYCEROL
3SFG1Ligand/IonSINEFUNGIN

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:315 , TYR A:324 , LYS A:333 , TYR A:334 , GLY A:365 , GLY A:367 , PRO A:370 , GLU A:392 , LYS A:393 , SER A:418 , ASP A:419 , MET A:420 , GLU A:435 , LEU A:436 , CYS A:449 , 3XV A:702 , HOH A:819 , HOH A:820 , HOH A:904binding site for residue SFG A 701
2AC2SOFTWAREGLN A:309 , LEU A:319 , PHE A:327 , LYS A:333 , GLU A:435 , LEU A:437 , SER A:439 , GLU A:444 , VAL A:503 , PHE A:577 , SER A:578 , TRP A:579 , PHE A:580 , SFG A:701 , HOH A:817binding site for residue 3XV A 702
3AC3SOFTWAREPHE A:40 , THR A:80 , GLN A:263binding site for residue GOL A 703
4AC4SOFTWAREARG A:52 , GLU A:53 , PHE A:54 , LYS A:60 , GLN A:66 , GLN A:109 , HOH A:908binding site for residue GOL A 704
5AC5SOFTWARETYR A:297 , GLY A:575binding site for residue GOL A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X60)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:57 -Pro A:58
2Gly A:64 -Pro A:65
3Ile A:464 -Pro A:465
4His A:523 -Pro A:524
5Ala A:619 -Pro A:620
6Ala B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X60)

(-) Exons   (0, 0)

(no "Exon" information available for 4X60)

(-) 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:625
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh..eeeee.............hhhhh......hhhhhhhhhhhhheeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eeeeeee..hhhhh................hhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhh...eeeeeee.hhhee.....ee.hhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhh.....hhhhhhh..................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhh.eeeee...........eeeee...........hhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhh........hhhhh..ee......ee....eeeeeee...........eeeeeeee....eeeeeeeeeeeeeee..eeee.hhhhh.........eeeeeeeeeee....eeeeeeeeee...eeeeeeeeee.......hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x60 A  13 RVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL 637
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632     

Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee.....eeeeee........eeeeee.hhhhh.hhhhh.eeeee...eeeeeee...eeeeee...eeeeeee......eeeeeeee.....eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee......eee.........eeeeee......eeeeee...eeeeee.....eeeeee.....eeeeee.......eeeee....eeee.....eeeee......eeeeee......eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x60 B  19 LPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVP 328
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328

   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 4X60)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X60)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X60)

(-) Gene Ontology  (51, 62)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:619 - Pro A:620   [ RasMol ]  
    Ala B:67 - Pro B:68   [ RasMol ]  
    Glu A:57 - Pro A:58   [ RasMol ]  
    Gly A:64 - Pro A:65   [ RasMol ]  
    His A:523 - Pro A:524   [ RasMol ]  
    Ile A:464 - Pro A:465   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM5_HUMAN | O147444gqb 4x61 4x63 5c9z 5emj 5emk 5eml 5emm 5fa5
        MEP50_HUMAN | Q9BQA14gqb 4x61 4x63 5c9z 5emj 5emk 5eml 5emm 5fa5

(-) Related Entries Specified in the PDB File

4x61 4x63