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(-) Description

Title :  CRYSTAL STRUCTURE OF HETEROCHROMATIN PROTEIN SIR3 IN COMPLEX WITH A SILENCED YEAST NUCLEOSOME
 
Authors :  F. Wang, G. Li, A. Mohammed, C. Lu, M. Currie, A. Johnson, D. Moazed
Date :  08 Mar 13  (Deposition) - 15 May 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Bah Domain, Silencing, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, G. Li, M. Altaf, C. Lu, M. A. Currie, A. Johnson, D. Moazed
Heterochromatin Protein Sir3 Induces Contacts Between The Amino Terminus Of Histone H4 And Nucleosomal Dna.
Proc. Natl. Acad. Sci. Usa V. 110 8495 2013
PubMed-ID: 23650358  |  Reference-DOI: 10.1073/PNAS.1300126110

(-) Compounds

Molecule 1 - HISTONE H3
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: HHT1, HHT2, HISTONE H3, N2749, SIN2, YBR010W, YBR0201, YNL031C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - HISTONE H4
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: HHF1, HHF2, HISTONE H4, N2752, YBR009C, YBR0122, YNL030W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 3 - HISTONE H2A.2
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: H2A2, HISTONE H2A.2, HTA2, YBL003C, YBL0103
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 4 - HISTONE H2B.2
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: H2B2, HISTONE H2B.2, HTB2, YBL002W, YBL0104
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 5 - REGULATORY PROTEIN SIR3
    Chains: K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SILENT INFORMATION REGULATOR 3
 
Molecule 6 - DNA (146-MER)
    Chains: I
    Engineered: YES
    Synthetic: YES
 
Molecule 7 - DNA (146-MER)
    Chains: J
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4JJN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Arg A:134 -Ser A:135
2His E:39 -Arg E:40
3Gly F:13 -Gly F:14
4Lys G:120 -Ser G:121
5Ser K:31 -Arg K:32
6Gln L:19 -Gly L:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JJN)

(-) 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:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh........hhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4jjn A  38 PHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS 135
                                    47        57        67        77        87        97       107       117       127        


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains d4jjnb_ B: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4jjn B  14 GAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 102
                                    23        33        43        53        63        73        83        93         


Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains d4jjnc_ C: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhh..eee.........hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4jjn C  14 ASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLP 118
                                    23        33        43        53        63        73        83        93       103       113     


Chain D from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains d4jjnd_ D: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4jjn D  34 KVRKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSST 128
                                    43        53        63        73        83        93       103       113       123     


Chain E from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4jjn E  39 HRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGER 134
                                    48        58        68        78        88        98       108       118       128      


Chain F from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains d4jjnf_ F: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4jjn F  12 KGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 102
                                    21        31        41        51        61        71        81        91       101 


Chain G from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4jjng_ G: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhh..eee.........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4jjn G  16 QSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKS 121
                                    25        35        45        55        65        75        85        95       105       115      


Chain H from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains d4jjnh_ H: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4jjn H  37 KETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSST 128
                                    46        56        66        76        86        96       106       116       126  


Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 4jjn I   2 TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 4jjn J   1 ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGA 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain K from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4jjnk_ K: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee................eeeeee.....ee....eeeeee....eeeeeeeeeee........eeeeeeeehhhhhhhhhhh...hhhhhh...hhhhhhhhh.......eeeeeeeeeeehhh.eeee.eee................eeeeeee........ee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jjn K   2 AKDLDGWQVIITDDQVIDDNNRRRSRKENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSNEYLKRVSVP 214
                            ||      14    ||  26      ||39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                            2|           19|         33|                                                                                                                                                                                 
                             6            22          37                                                                                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4jjnl_ L: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.................eeeeee.....ee....eeeeee....eeeeeeeeeeee......eeeeeeeeehhhhhhhhhhh...hhhhhh...hhhhhhhhhhh.....eeeeeeeeeeehhh.eeee.ee.hhhhhh..........eeeeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jjn L   4 TLKDLDGWQVIITDDQGRVIRRRSRKRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSNEYLKRVSVPVSGQ 218
                                    13        23|       37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 
                                              23|                                                                                                                                                                                              
                                               28
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 68)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:134 - Ser A:135   [ RasMol ]  
    Gln L:19 - Gly L:20   [ RasMol ]  
    Gly F:13 - Gly F:14   [ RasMol ]  
    His E:39 - Arg E:40   [ RasMol ]  
    Lys G:120 - Ser G:121   [ RasMol ]  
    Ser K:31 - Arg K:32   [ RasMol ]  
 

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  4jjn
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  H2A2_YEAST | P04912
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  H2B2_YEAST | P02294
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  H3_YEAST | P61830
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  H4_YEAST | P02309
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  SIR3_YEAST | P06701
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A2_YEAST | P04912: 4kud
        H2B2_YEAST | P02294: 1id3 2fsb
        H3_YEAST | P61830: 1id3 1m1d 1peg 1pu9 1pua 1qsn 2cnx 2h2g 2idc 2jmj 2rnw 2rnx 2rsn 3mp1 3mp6 3q33 4kud 4psx 5d7e 5iok
        H4_YEAST | P02309: 1e6i 1id3 1q1a 1szc 1szd 2dvq 2dvr 2e3k 2fsb 2h2h 2l5a 2qqf 2qqg 3to6 4kud 4psx 4twi 4twj
        SIR3_YEAST | P06701: 2fl7 2fvu 3owt 3te6 3tu4 3zco 4kud 4kui 4kul 4ld9

(-) Related Entries Specified in the PDB File

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