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(-) Description

Title :  STRUCTURE OF AN RSP5XUBXSNA3 COMPLEX: MECHANISM OF UBIQUITIN LIGATION AND LYSINE PRIORITIZATION BY A HECT E3
 
Authors :  H. B. Kamadurai, D. Miller, B. A. Schulman
Date :  21 Jun 13  (Deposition) - 14 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Ligase, E3, Rsp5, Nedd4, Ubiquitin, Hect, Sna3, Thioester, Maleimide, Crosslink, Ligase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. B. Kamadurai, Y. Qiu, A. Deng, J. S. Harrison, C. Macdonald, M. Actis P. Rodrigues, D. J. Miller, J. Souphron, S. M. Lewis, I. Kurinov, N. Fujii, M. Hammel, R. Piper, B. Kuhlman, B. A. Schulman
Mechanism Of Ubiquitin Ligation And Lysine Prioritization B A Hect E3.
Elife V. 2 00828 2013
PubMed-ID: 23936628  |  Reference-DOI: 10.7554/ELIFE.00828

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RSP5
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: WW3 + HECT (UNP RESIDUES 383-809)
    Gene: MDP1, NPI1, RSP5, SYGP-ORF41, YER125W
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: REVERSES SPT-PHENOTYPE PROTEIN 5
 
Molecule 2 - PROTEIN SNA3
    Chains: C, D
    Engineered: YES
    Fragment: CYTOSOLIC FRAGMENT (UNP RESIDUES 104-127)
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Synthetic: YES
 
Molecule 3 - UBIQUITIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-75
    Gene: UBC, UBIQUITIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4LCD)

(-) Sites  (0, 0)

(no "Site" information available for 4LCD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LCD)

(-) 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:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.......eeee....eee..............hhhhhhhhhhhhhhh.hhhhh....eeeeeehhhhhhhhhhhhhhh...hhhhheeeeee....hhhhhhhhhhhhhhhhhhhh.eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhh............ee.eeeeee..eeeeee........ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhh....hhhhhhhheeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh........eeee.........ee.....eee.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcd A 383 VSQLGPLPSGWEMRLTNTARVYFVDHNTKTTTWDDPRLPSSLDQNVPQYKRDFRRKVIYFRSQPALRILPGQLHIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGYGGVSREFFFLLSHEMFNPFYGLFEYSAYDNYTIQINPNSGINPEHLNYFKFIGRVVGLGVFHRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDGVLDLTFSADDERFGEVVTVDLKPDGRNIEVTDGNKKEYVELYTQWRIVDRVQEQFKAFMDGFNELIPEDLVTVFDERELELLIGGIAEIDIEDWKKHTDYRGYQESDEVIQWFWKAVSEWDNEQRARLLQFTTGTSRIPVNGFKDLQGSDGPRRFTIEKAGEVQQLPKSHTCFNRVDLPQYVDYDSMKQKLTLAVEETIGF 806
                                   392       402       412       422       432       442       452       462       472       482       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797         
                                                                                                                                     490|                                                                                                                                                                                                                                                                                                                      
                                                                                                                                      496                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.....eeeee....eee..............hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..hhhhhhhhhhhh.hhhhhheeeeeeee......hhhhhhhhhhhhhhhh.eee.......eee..hhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhh......eeeeee..eeeeee...hhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhh....hhhhhhh.ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh........ee...........eeehhhheee.....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcd B 384 SQLGPLPSGWEMRLTNTARVYFVDHNTKTTTWDDPRLPSSLDQNVPQYKRDFRRKVIYFRSQPALRILPGQLHIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGGGVSREFFFLLSHEMFNPFYGLFEYSAYDNYTIQINPNSGINPEHLNYFKFIGRVVGLGVFHRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDLTFSADDERFGEVVTVDLKPDGRNIEVTDGNKKEYVELYTQWRIVDRVQEQFKAFMDGFNELIPEDLVTVFDERELELLIGGIAEIDIEDWKKHTDYRGYQESDEVIQWFWKAVSEWDNEQRARLLQFTTGTSRIPVNGFKDLQGSDGPRRFTIEKAGEVQQLPKSHTCFNRVDLPQYVDYDSMKQKLTLAVEETIGF 806
                                   393       403       413       423       433       443       453       463       473       483      |499       509       519       529       539       549       559       569       579       589       599    || 613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803   
                                                                                                                                    490|                                                                                                        604|                                                                                                                                                                                                     
                                                                                                                                     497                                                                                                         609                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               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
                 4lcd C 105 QPPAYDED 112


Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 4lcd D 104 AQPPAYDEDDEAGA 117
                                   113    


Chain E from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eee.......hhhhhhhhhhhhhh.....eeee....................eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4lcd E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRC  75
                                    10        20        30        40        50        60        70     


Chain F from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.....eeee......................eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4lcd F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRC  75
                                    10        20        30        40        50        60        70
   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 4LCD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (135, 144)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RSP5_YEAST | P39940: 3olm 5hpl
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

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