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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINALLY ACETYLATED BAH DOMAIN OF SIR3 BOUND TO THE NUCLEOSOME CORE PARTICLE
 
Authors :  N. Arnaudo, I. S. Fernandez, S. H. Mclaughlin, S. Y. Peak-Chew, D. Rhode F. Martino
Date :  24 Jun 13  (Deposition) - 14 Aug 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Beta Barrel, Protein-Dna Complex, Double Helix, Alpha-Helix, Beta- Sheet, Double Stranded Dna, Chromatin Binding, Chromatin, N-Terminal Acetylation, Nucleus, Nuclear Protein-Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Arnaudo, I. S. Fernandez, S. H. Mclaughlin, S. Y. Peak-Chew, D. Rhodes, F. Martino
The N-Terminal Acetylation Of Sir3 Stabilizes Its Binding T The Nucleosome Core Particle.
Nat. Struct. Mol. Biol. V. 20 1119 2013
PubMed-ID: 23934150  |  Reference-DOI: 10.1038/NSMB.2641

(-) Compounds

Molecule 1 - HISTONE H3.2
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 2 - HISTONE H4
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 3 - HISTONE H2A
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LOC494591
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 4 - HISTONE H2B 1.1
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: H2B1.1
 
Molecule 5 - WIDOM 601 SEQUENCE REVERSE
    Chains: I
    Engineered: YES
    Other Details: THIS SEQUENCE HAS BEEN SELECTED IN VITRO
    Synthetic: YES
 
Molecule 6 - WIDOM 601 SEQUENCE FORWARD
    Chains: J
    Engineered: YES
    Other Details: THIS SEQUENCE HAS BEEN SELECTED IN VITRO
    Synthetic: YES
 
Molecule 7 - REGULATORY PROTEIN SIR3
    Chains: K, L
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SILENT INFORMATION REGULATOR 3

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 4LD9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LD9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:37 -Pro A:38
2Asn K:27 -Arg K:28
3Ser K:162 -Ile K:163
4Pro K:214 -Val K:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LD9)

(-) Exons   (0, 0)

(no "Exon" information available for 4LD9)

(-) 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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4ld9 A  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 133
                                    46        56        66        76        86        96       106       116       126       


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4ld9 B  12 KGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100
                                    21        31        41        51        61        71        81        91         


Chain C from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhh...ee.........hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4ld9 C  20 RAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP 117
                                    29        39        49        59        69        79        89        99       109        


Chain D from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4ld9 D  38 YAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT 123
                                    47        57        67        77        87        97       107       117      


Chain E from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4ld9 E  44 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 133
                                    53        63        73        83        93       103       113       123       133


Chain F from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh......ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4ld9 F  18 HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100
                                    27        37        47        57        67        77        87        97   


Chain G from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh..hhhhhh...ee.........hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4ld9 G  18 SSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP 117
                                    27        37        47        57        67        77        87        97       107       117


Chain H from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4ld9 H  35 KESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKY 122
                                    44        54        64        74        84        94       104       114        


Chain I from PDB  Type:DNA  Length:143
                                                                                                                                                                               
                 4ld9 I -72 ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTG  70
                                   -63       -53       -43       -33       -23       -13        -3         7        17        27        37        47        57        67   


Chain J from PDB  Type:DNA  Length:142
                                                                                                                                                                              
                 4ld9 J -69 AGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT  72
                                   -60       -50       -40       -30       -20       -10         0        10        20        30        40        50        60        70  


Chain K from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee..................eeeee......ee....eeeeee....eeeeeeeeeeee......eeeeeeeee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeeeeeeeee.....eeee.eeehhhhhh.........eeeeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld9 K   1 xAKTLKDLDGWQVIITDDQGRVIDDNNRRRRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSVPV 215
                            |       10        20        30|       43        53        63        73        83        93       103       113       123       133       143       153       163|      174       184       194       204       214 
                            1-ACE                       30|                                                                                                                              163|                                                  
                                                         34                                                                                                                               165                                                  


Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeee..............eeeee......ee....eeeeee....eeeeeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeeeeee.hhh.eee..eee.hhhhhh.........eeeeeeee.......ee.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld9 L   1 xAKTLKDLDGWQVIITDDQGRVIDDNNRRENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSV 213
                            |       10        20        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
                            1-ACE                      29|                                                                                                                                                                                
                                                        37
   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 4LD9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LD9)

(-) Gene Ontology  (27, 51)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1_XENLA | P06897: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2fj7 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3lja 3mnn 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5hq2 5mlu 5nl0
        H2B11_XENLA | P02281: 1aoi 1f66 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2nzd 3b6f 3b6g 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4kgc 4kha 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5hq2 5nl0 5x0x 5x0y
        H32_XENLA | P84233: 1f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3gv6 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        H4_XENLA | P62799: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        Q6AZJ8_XENLA | Q6AZJ8: 2nzd 3b6f 3b6g 3kuy 3kwq 3lja 3mnn 3tu4 3ut9 3uta 3utb 4j8v 4j8w 4j8x 4xuj 4xzq 4ys3 4z66 5cp6 5dnm 5dnn 5e5a 5hq2
        SIR3_YEAST | P06701: 2fl7 2fvu 3owt 3te6 3tu4 3zco 4jjn 4kud 4kui 4kul
UniProtKB/TrEMBL
        Q6AZJ8_XENLA | Q6AZJ8: 3kxb 3lel 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mvd 4kgc 4kha 4r8p 5x0x 5x0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LD9)