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(-) Description

Title :  STRUCTURE OF THE SAGA UBP8/SGF11(1-72, DELTA-ZNF)/SUS1/SGF73 DUB MODULE
 
Authors :  N. L. Samara, A. E. Ringel, C. Wolberger
Date :  11 Jun 12  (Deposition) - 25 Jul 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Domain-Swapping, Deubiquitination, Transcription, Nucleosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. L. Samara, A. E. Ringel, C. Wolberger
A Role For Intersubunit Interactions In Maintaining Saga Deubiquitinating Module Structure And Activity.
Structure V. 20 1414 2012
PubMed-ID: 22771212  |  Reference-DOI: 10.1016/J.STR.2012.05.015

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8
    Chains: A, E
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32A
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UBP8, YM9959.05, YMR223W
    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 - PROTEIN SUS1
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSF
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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 Plasmid: PCDFDUET-1
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES SGF11 1-72
    Gene: SGF11, YPL047W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: 11 KDA SAGA-ASSOCIATED FACTOR
 
Molecule 4 - SAGA-ASSOCIATED FACTOR 73
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-96
    Gene: SGF73, YGL066W
    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/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN14Ligand/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:339 , ASN A:340BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWAREARG A:468 , GLN A:469 , LEU G:23 , HIS H:48 , ASP H:67BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWARECYS D:78 , CYS D:81 , HIS D:93 , HOH D:203BINDING SITE FOR RESIDUE ZN D 101
09AC9SOFTWARECYS E:4 , HIS E:6 , CYS E:96 , CYS E:99BINDING SITE FOR RESIDUE ZN E 501
10BC1SOFTWARECYS E:46 , CYS E:49 , CYS E:68 , HIS E:73BINDING SITE FOR RESIDUE ZN E 502
11BC2SOFTWARECYS E:60 , CYS E:63 , HIS E:77 , HIS E:83BINDING SITE FOR RESIDUE ZN E 503
12BC3SOFTWAREHIS E:170 , CYS E:174 , CYS E:182 , CYS E:185BINDING SITE FOR RESIDUE ZN E 504
13BC4SOFTWAREHIS E:250 , CYS E:271 , CYS E:273 , HIS E:276BINDING SITE FOR RESIDUE ZN E 505
14BC5SOFTWARECYS E:289 , CYS E:292 , CYS E:336 , CYS E:339BINDING SITE FOR RESIDUE ZN E 506
15BC6SOFTWARECYS H:78 , CYS H:81 , HIS H:93 , HOH H:202BINDING SITE FOR RESIDUE ZN H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Gln A:228 -Asn A:229
2Leu A:230 -Ala A:231
3Ala A:231 -Gly A:232
4Ala A:266 -Asn A:267
5Asn A:268 -Lys A:269
6Thr B:5 -Ala B:6
7Pro D:27 -Ser D:28
8Gln E:228 -Asn E:229
9Leu E:230 -Ala E:231
10Ala E:231 -Gly E:232
11Ser E:234 -Gln E:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FJC)

(-) 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:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               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..................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..............hhhhhhh.eeeeeeee......eeeeeeeee..eee......hhhhhhhhhhh.eee..............eeeeeeeee...eeeeee..eee.....eee.........eee.hhhh......eeeeeeeeeeeee....eeeeeeeee...eeeeee..eeeeehhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fjc A   0 AMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGATNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       211       221       231       241       251       261|      273       283       293       303       313       323       333  ||   344       354       364       374       384       394|      414       424       434       444       454       464       
                                                                                                                                                                                                                               197|                                                261|                                                                     336|                                                     394|                                                                  
                                                                                                                                                                                                                                210                                                 264                                                                      338                                                      405                                                                  


Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhheee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4fjc B   5 TAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ  96
                                    14        24        34        44        54        64        74        84        94  


Chain C from PDB  Type:PROTEIN  Length:43
                                                                           
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 4fjc C   3 EETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDL  45
                                    12        22        32        42   


Chain D from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeehhhhhhhh.........hhhhhhhhhhh........hhhhhhhhh................eeee.....eeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4fjc D   5 DAEIKGIKPKVIEEYSLSQGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN  96
                                    14        26        36        46        56        66        76        86        96
                                             23|                                                                      
                                              26                                                                      


Chain E from PDB  Type:PROTEIN  Length:434
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.............eeee.....eee...hhhhhhhhhhh..eeee.....eee....ee...hhhhhhhhhhhhhhhhhhhee..............hhhhhhhhhhhh.hhhhhhhhhh..............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...............eeeeeeee......eeeeeeeee.eeeee.....hhhhhhhhhh.eeeeeeeeeee....eeeeeeeeeeeee...eeeeeee.................eee.hhhh......eeeeeeeeeeee......eeeeeee.....eeeee..eeeeehhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fjc E   0 AMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLNRKLDDFIEFPTYLNMKNYCSTKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139|      153       163       173       183       193     ||214       224       234       244       254    || 273       283       293       303       313       323       333       343       353       363    || 377       387      |407       417       427       437       447       457       467    
                                                                                                                                                                     139|                                                    199|                                             259|                                                                                                368|                  394|                                                                  
                                                                                                                                                                      144                                                     211                                              269                                                                                                 373                   405                                                                  


Chain F from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4fjc F   7 QLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIV  93
                                    16        26        36        46        56        66        76        86       


Chain G from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 4fjc G   5 TITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDL  45
                                    14        24        34        44 


Chain H from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhh.......hhhhhhhhh................eeee.....eee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4fjc H   9 KGIKPKVIEEYDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLE  95
                                    18||      38        48        58        68        78        88       
                                     19|                                                                 
                                      30
   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 4FJC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 82)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:231 - Gly A:232   [ RasMol ]  
    Ala A:266 - Asn A:267   [ RasMol ]  
    Ala E:231 - Gly E:232   [ RasMol ]  
    Asn A:268 - Lys A:269   [ RasMol ]  
    Gln A:228 - Asn A:229   [ RasMol ]  
    Gln E:228 - Asn E:229   [ RasMol ]  
    Leu A:230 - Ala A:231   [ RasMol ]  
    Leu E:230 - Ala E:231   [ RasMol ]  
    Pro D:27 - Ser D:28   [ RasMol ]  
    Ser E:234 - Gln E:235   [ RasMol ]  
    Thr B:5 - Ala B:6   [ RasMol ]  
 

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  4fjc
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  SGF11_YEAST | Q03067
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  SGF73_YEAST | P53165
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  SUS1_YEAST | Q6WNK7
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  UBP8_YEAST | P50102
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 Related Entries

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

UniProtKB/Swiss-Prot
        SGF11_YEAST | Q03067: 2lo2 3kik 3kjl 3m99 3mhh 3mhs 4fip 4fk5 4wa6 4zux
        SGF73_YEAST | P53165: 2lo3 3m99 3mhh 3mhs 4fip 4fk5 4w4u 4wa6 4zux
        SUS1_YEAST | Q6WNK7: 3fwb 3fwc 3kik 3kjl 3m99 3mhh 3mhs 4c31 4fip 4fk5 4mbe 4wa6 4zux
        UBP8_YEAST | P50102: 3m99 3mhh 3mhs 4fip 4fk5 4wa6 4zux

(-) Related Entries Specified in the PDB File

4fip SAME COMPLEX BUT WITH AN S144N MUTATION IN UBP8.