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(-) Description

Title :  STRUCTURE OF YEAST SAGA DUBM WITH SGF73 N59D MUTANT AT 2.36 ANGSTROMS RESOLUTION
 
Authors :  C. Wolberger, M. Yan
Date :  28 Aug 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,E  (1x)
Biol. Unit 2:  D,F,G,H  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x)
Keywords :  Multi-Protein Complex, Hydrolase-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wolberger, M. Yan
Structure Of Yeast Saga Dubm With Sgf73 N59D Mutant At 2. 36 Angstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8
    Chains: A, D
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBP8, YMR223W, YM9959.05
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DEUBIQUITINATING ENZYME 8,UBIQUITIN THIOESTERASE 8, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 8
 
Molecule 2 - TRANSCRIPTION AND MRNA EXPORT FACTOR SUS1
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SUS1, YBR111W-A
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 3 - SAGA-ASSOCIATED FACTOR 11
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SGF11, SCY_5678
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 307796
    Strain: YJM789
 
Molecule 4 - SAGA-ASSOCIATED FACTOR 73
    Chains: E, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SGF73, YGL066W
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: 73 KDA SAGA-ASSOCIATED FACTOR,SAGA HISTONE ACETYLTRANSFERASE COMPLEX 73 KDA SUBUNIT

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABC E   
Biological Unit 2 (1x):    D FGH
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1ZN15Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:4 , HIS A:6 , CYS A:96 , CYS A:99binding site for residue ZN A 501
02AC2SOFTWARECYS A:46 , CYS A:49 , CYS A:68 , HIS A:73binding site for residue ZN A 502
03AC3SOFTWARECYS A:60 , CYS A:63 , HIS A:77 , HIS A:83binding site for residue ZN A 503
04AC4SOFTWAREHIS A:170 , CYS A:174 , CYS A:182 , CYS A:185binding site for residue ZN A 504
05AC5SOFTWAREHIS A:250 , CYS A:271 , CYS A:273 , HIS A:276binding site for residue ZN A 505
06AC6SOFTWARECYS A:289 , CYS A:292 , CYS A:336 , CYS A:339binding site for residue ZN A 506
07AC7SOFTWAREHIS C:88 , CYS C:92binding site for residue ZN C 101
08AC8SOFTWARECYS E:78 , CYS E:81 , HIS E:93 , HOH E:203binding site for residue ZN E 101
09AC9SOFTWARECYS D:4 , HIS D:6 , CYS D:96 , CYS D:99binding site for residue ZN D 501
10AD1SOFTWARECYS D:46 , CYS D:49 , CYS D:68 , HIS D:73binding site for residue ZN D 502
11AD2SOFTWARECYS D:60 , CYS D:63 , HIS D:77 , HIS D:83binding site for residue ZN D 503
12AD3SOFTWAREHIS D:170 , CYS D:174 , CYS D:182 , CYS D:185binding site for residue ZN D 504
13AD4SOFTWAREHIS D:250 , CYS D:271 , CYS D:273 , HIS D:276binding site for residue ZN D 505
14AD5SOFTWARECYS G:73 , CYS G:76 , HIS G:88 , CYS G:92binding site for residue ZN G 101
15AD6SOFTWARECYS H:78 , CYS H:81 , HIS H:93 , HOH H:201binding site for residue ZN H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WA6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WA6)

(-) Exons   (0, 0)

(no "Exon" information available for 4WA6)

(-) 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:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh............eeee.....eee...hhhhhhhhhhh..eeee.....eee....ee...hhhhhhhhhhhhhhhhhhhee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhh.eeeeeeee..........eeeee..eee......hhhhhhhhhhh.ee.................eeeeeeee...eeeeee..eee.....eee.........eee.hhhh......eeeeeeeeeeeee....eeeeeeee.hhh.eeeee..eeeeehhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wa6 A   1 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNRQTGFIYLLTCAWKIQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       212       222   ||  241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  ||   411       421       431       441       451       461       471
                                                                                                                                                                                                                               198|            226|                                                                                                                                                           394|                                                                  
                                                                                                                                                                                                                                211             236                                                                                                                                                            405                                                                  


Chain B from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4wa6 B   1 MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ  96
                                    10        20        30        40        50        60        70        80        90      


Chain C from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4wa6 C   5 TITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDINGLQKQQESSQYIVSANRLAAHLQRCLS  94
                                    14        24        34        44        54        64      ||82        92  
                                                                                             71|              
                                                                                              80              


Chain D from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh............eeee.....eee...hhhhhhhhhhh..eeee.....eee....ee...hhhhhhhhhhhhhhhhhhhee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhh.eeeeee...eeeeee..eee......hhhhhhhhhhh....eeeeee...eeeeee..eee.....eee.........eee.hhhh.....eeeeeeeeeeeee....eeeeeeee.....eeeee..eeeeehhhhhhh....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wa6 D   1 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTNRQTGFIYLLTCAWKIQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSISKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       210       220     ||239       249       259       269       279       297       307       317       327|      355       365       375       385       406       416       426       436       446       456       466     
                                                                                                                                                                                                                                199|             226|                                                287|                            327|                                            393|                                                                  
                                                                                                                                                                                                                                 210              236                                                 296                             346                                             405                                                                  


Chain E from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhh....hhhhhhhhhhh........hhhhhhhhh........hhhhh...eeee.....eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4wa6 E   2 RSGDAEIKGIKPKVIEEYSDSWKSLMSSAKDTPLQYDHMNRESLKKYFDPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLE  95
                                    11        30        40        50        60        70        80        90     
                                             20|                                                                 
                                              30                                                                 


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4wa6 F   3 MDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT  95
                                    12        22        32        42        52        62        72        82        92   


Chain G from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....eee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4wa6 G   1 MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYIHCENCGRDVSNRLAAHLQRCLS  94
                                    10        20        30        40      ||72        83        93 
                                                                         47|         81|           
                                                                          70          83           


Chain H from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhhh..hhhhhhhhhhh........hhhhhhhhh................eeee.....eee..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4wa6 H   4 GDAEIKGIKPKVIEEDSWKSLMSSAKDTPLQYDHMNRESLKKYFDPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN  96
                                    13    ||  34        44        54        64        74        84        94  
                                         18|                                                                  
                                          30
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  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 4WA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WA6)

(-) Gene Ontology  (49, 92)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SGF11_YEAS7 | A6ZWK1: 4zux
        SGF11_YEAST | Q03067: 2lo2 3kik 3kjl 3m99 3mhh 3mhs 4fip 4fjc 4fk5 4zux
        SGF73_YEAST | P53165: 2lo3 3m99 3mhh 3mhs 4fip 4fjc 4fk5 4w4u 4zux
        SUS1_YEAST | Q6WNK7: 3fwb 3fwc 3kik 3kjl 3m99 3mhh 3mhs 4c31 4fip 4fjc 4fk5 4mbe 4zux
        UBP8_YEAST | P50102: 3m99 3mhh 3mhs 4fip 4fjc 4fk5 4zux

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WA6)