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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX
 
Authors :  S. Antonysamy, Z. Bonday, R. Campbell, B. Doyle, Z. Druzina, T. Gheyi, B L. N. Jungheim, Y. Qian, C. Rauch, M. Russell, J. M. Sauder, S. R. Wasser K. Weichert, F. S. Willard, A. Zhang, S. Emtage
Date :  22 Aug 12  (Deposition) - 17 Oct 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (4x)
Keywords :  Tim Barrel, Beta-Propeller, Methyltransferase, Methylation, Transferase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Antonysamy, Z. Bonday, R. M. Campbell, B. Doyle, Z. Druzina, T. Gheyi, B. Han, L. N. Jungheim, Y. Qian, C. Rauch, M. Russell, J. M. Sauder, S. R. Wasserman, K. Weichert, F. S. Willard, A. Zhang, S. Emtage
Crystal Structure Of The Human Prmt5:Mep50 Complex.
Proc. Natl. Acad. Sci. Usa V. 109 17960 2012
PubMed-ID: 23071334  |  Reference-DOI: 10.1073/PNAS.1209814109

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 5
    ChainsA
    EC Number2.1.1.-, 2.1.1.125
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    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, SKB1 HOMOLOG, SKB1HS, PROTEIN ARGININE N- METHYLTRANSFERASE 5, N-TERMINALLY PROCESSED
 
Molecule 2 - METHYLOSOME PROTEIN 50
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GeneWDR77, MEP50, HKMT1069, NBLA10071
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMEP-50, ANDROGEN RECEPTOR COFACTOR P44, WD REPEAT-CONTAINING PROTEIN 77, P44/MEP50
 
Molecule 3 - HISTONE H4 PEPTIDE
    ChainsC
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (4x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
10XU1Ligand/Ion(2S,5S,6E)-2,5-DIAMINO-6-[(3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYDIHYDROFURAN-2(3H)-YLIDENE]HEXANOIC ACID
2ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
10XU4Ligand/Ion(2S,5S,6E)-2,5-DIAMINO-6-[(3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYDIHYDROFURAN-2(3H)-YLIDENE]HEXANOIC ACID
2ACE4Mod. Amino AcidACETYL GROUP

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:314 , LEU A:315 , TYR A:324 , LYS A:333 , TYR A:334 , GLY A:365 , PRO A:370 , LEU A:371 , GLU A:392 , LYS A:393 , SER A:418 , ASP A:419 , MET A:420 , GLU A:435 , LEU A:436 , GLU A:444 , CYS A:449 , HOH A:832 , HOH A:920 , HOH A:947 , HOH A:1024 , ARG C:3BINDING SITE FOR RESIDUE 0XU A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GQB)

(-) 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:625
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhh...eeeee.............hhhhh......hhhhhhhhhhhhheeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eeeeeee..hhhhhh...............hhhhhhhhhhhhhhhhh.....eeeeee......hhhhhhh.....eeeeeee.hhhee.....ee.hhhhhhhhhhhhhh..eeeee....hhhhh.hhhhhhhhhhhhh....hhhhhhh........ee........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh.eeeee...........eeeee.......hhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeehhhhhhhhhh........hhhhhh.ee......ee....eeeeeee...........eeeeeeee....eeeeeeeeeeeeeee..eeee.hhhhh.........eeeeeeeeeee....eeeeeeeeee...eeeeeeeeee.......hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqb 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:303
                                                                                                                                                                                                                                                                                                                                               
               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.....eeee.....eeeeee.......eeeee....eeee.....eeeee......eeeeee......eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqb B  21 PNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPT 329
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |214       224       234       244|      256       266       276       286       296       306       316       326   
                                                                                                                                                                                                                    207|                             244|                                                                                  
                                                                                                                                                                                                                     212                              247                                                                                  

Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ....ee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4gqb C   0 xSGRGKGGK   8
                            |        
                            0-ACE    

   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 4GQB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 93)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM5_HUMAN | O147444x60 4x61 4x63 5c9z 5emj 5emk 5eml 5emm 5fa5
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x
        MEP50_HUMAN | Q9BQA14x60 4x61 4x63 5c9z 5emj 5emk 5eml 5emm 5fa5

(-) Related Entries Specified in the PDB File

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