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(-) Description

Title :  STRUCTURE OF THE SAGA UBP8(S144N)/SGF11(1-72, DELTA-ZNF)/SUS1/SGF73 DUB MODULE
 
Authors :  N. L. Samara, A. E. Ringel, C. Wolberger
Date :  10 Jun 12  (Deposition) - 25 Jul 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Domain-Swapping, Deubiquitination, Transcription, Nucleosomes, 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
    Mutation: YES
    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
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 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
    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  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1ZN14Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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:250 , CYS A:271 , CYS A:273 , HIS A:276BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREHIS A:170 , CYS A:174 , CYS A:182 , CYS A:185BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWARECYS A:289 , CYS A:292 , CYS A:336 , CYS A:339BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWARECYS D:78 , CYS D:81 , HIS D:93BINDING SITE FOR RESIDUE ZN D 101
08AC8SOFTWAREHIS E:170 , CYS E:174 , CYS E:182 , CYS E:185BINDING SITE FOR RESIDUE ZN E 501
09AC9SOFTWAREHIS E:250 , CYS E:271 , CYS E:273 , HIS E:276BINDING SITE FOR RESIDUE ZN E 502
10BC1SOFTWARECYS E:46 , CYS E:49 , CYS E:68 , HIS E:73BINDING SITE FOR RESIDUE ZN E 503
11BC2SOFTWARECYS E:289 , CYS E:292 , CYS E:336 , CYS E:339BINDING SITE FOR RESIDUE ZN E 504
12BC3SOFTWARECYS E:60 , CYS E:63 , HIS E:77 , HIS E:83BINDING SITE FOR RESIDUE ZN E 505
13BC4SOFTWARECYS E:4 , HIS E:6 , CYS E:96 , CYS E:99BINDING SITE FOR RESIDUE ZN E 506
14BC5SOFTWARECYS H:78 , CYS H:81 , HIS H:93 , HOH H:203BINDING SITE FOR RESIDUE ZN H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser A:296 -Lys A:297
2Gly D:24 -Ser D:25
3Gln E:80 -Ile E:81
4Asn E:268 -Lys E:269
5Cys E:339 -Asn E:340
6Lys E:420 -Gly E:421
7Asp E:444 -Ser E:445

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FIP)

(-) 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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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...hhhhhhhhhh...hhhhhhhheeeeeeee.........eeeeee..eee......hhhhhhhhhh.....................eeeeeeee...eeeeee..eee.....eee.........eee.hhhh..........eeeeeeeeeeee......eeeeeeee...eeeeee..eeeeehhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fip A   0 AMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTNRQTGFIYLLTCAWKINQNQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|      219       229|      245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       401       411       421       431       441       451       461       471
                                                                                                                                                                                                                                 199|                229|                                                                                                                                                           394|                                                                      
                                                                                                                                                                                                                                  210                 236                                                                                                                                                            401                                                                      


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4fip B   6 AQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT  95
                                    15        25        35        45        55        65        75        85        95


Chain C 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
                 4fip C   5 TITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDL  45
                                    14        24        34        44 


Chain D from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..........hhhhhhhhhh........hhhhhhhhh................eeee.....eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4fip D   5 DAEIGIKPKVIEEYSLGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLE  95
                               ||   15     || 27        37        47        57        67        77        87        
                               8|         21|                                                                       
                               10          24                                                                       


Chain E from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh............eeee.....eee...hhhhhhhhh....eeee.....eee....eee..hhhhhhhhhhhhhhhhhhhee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.eeeeeeee......eeeeeeeee..eeee.....hhhhhhhhhh.eeeeeeeeee......eeeeeeeeeeee...eeeeeee.eee.....eee.........eee.hhhh......eeeeeeeeeeee......eeeeeee.hhh.eeeee..eeeeehhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fip E   1 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN 471
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       212       222       232       242       252      |270       280       290       300       310       320       330       340       350       360       370       380       390   ||  410       420       430       440       450       460       470 
                                                                                                                                                                                                                                199|                                            259|                                                                                                                           394|                                                                  
                                                                                                                                                                                                                                 212                                             268                                                                                                                            405                                                                  


Chain F from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4fip F   6 AQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT  95
                                    15        25        35        45        55        65        75        85        95


Chain G 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
                 4fip G   3 EETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDL  45
                                    12        22        32        42   


Chain H from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh......hhhhhhhhhh.........hhhhhhhhh................eeee.....eeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4fip H   6 AEIKGIKPKVIEEYSLDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN  96
                                    15     || 33        43        53        63        73        83        93   
                                          21|                                                                  
                                           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 4FIP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 82)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gln E:80 - Ile E:81   [ RasMol ]  
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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 4fjc 4fk5 4wa6 4zux
        SGF73_YEAST | P53165: 2lo3 3m99 3mhh 3mhs 4fjc 4fk5 4w4u 4wa6 4zux
        SUS1_YEAST | Q6WNK7: 3fwb 3fwc 3kik 3kjl 3m99 3mhh 3mhs 4c31 4fjc 4fk5 4mbe 4wa6 4zux
        UBP8_YEAST | P50102: 3m99 3mhh 3mhs 4fjc 4fk5 4wa6 4zux

(-) Related Entries Specified in the PDB File

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