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(-) Description

Title :  COMPLEX OF SNF2-NUCLEOSOME COMPLEX WITH SNF2 BOUND TO SHL2 OF THE NUCLEOSOME
 
Authors :  M. Li, X. Liu, X. Xia, Z. Chen, X. Li
Date :  23 Jan 17  (Deposition) - 19 Apr 17  (Release) - 07 Jun 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.69
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,O
Keywords :  Snf2, Nucleosome, Chromatin Remodeling, Structural Protein-Hydrolase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Liu, M. Li, X. Xia, X. Li, Z. Chen
Mechanism Of Chromatin Remodelling Revealed By The Snf2-Nucleosome Structure.
Nature V. 544 440 2017
PubMed-ID: 28424519  |  Reference-DOI: 10.1038/NATURE22036

(-) Compounds

Molecule 1 - HISTONE H3.2
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: AFRICAN CLAWED FROG
    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: AFRICAN CLAWED FROG
    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: HIST1H2AJ, LOC494591
    Organism Common: AFRICAN CLAWED FROG
    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: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: H2B1.1
 
Molecule 5 - DNA (167-MER)
    Chains: I
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 6 - DNA (167-MER)
    Chains: J
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 7 - TRANSCRIPTION REGULATORY PROTEIN SNF2
    Chains: O
    EC Number: 3.6.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 666-1400
    Gene: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ATP-DEPENDENT HELICASE SNF2,REGULATORY PROTEIN GAM1, REGULATORY PROTEIN SWI2,SWI/SNF COMPLEX COMPONENT SNF2,TRANSCRIPTION FACTOR TYE3

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric/Biological Unit : ABCDEFGHIJO

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5X0Y)

(-) Sites  (0, 0)

(no "Site" information available for 5X0Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X0Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5X0Y)

(-) 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 .......hhhhhhhhhhhhh......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                5x0y A   37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER  134
                                    46        56        66        76        86        96       106       116       126        


Chain B from PDB  Type:PROTEIN  Length:87
                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                5x0y B   15 AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG  101
                                    24        34        44        54        64        74        84        94       


Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhh.ee..........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5x0y C   12 AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK  118
                                    21        31        41        51        61        71        81        91       101       111       


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                5x0y D   29 TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA  121
                                    38        48        58        68        78        88        98       108       118   


Chain E from PDB  Type:PROTEIN  Length:95
                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......hhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                5x0y E   40 RYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER  134
                                    49        59        69        79        89        99       109       119       129     


Chain F from PDB  Type:PROTEIN  Length:86
                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh..ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                5x0y F   17 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  102
                                    26        36        46        56        66        76        86        96      


Chain G from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhh.............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5x0y G   12 AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK  118
                                    21        31        41        51        61        71        81        91       101       111       


Chain H from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                5x0y H   29 TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA  121
                                    38        48        58        68        78        88        98       108       118   


Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                   
                5x0y 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
                                                                                                                                                                                   
                5x0y J    1 ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGA  146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      


Chain O from PDB  Type:PROTEIN  Length:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhh...................hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..ee..hhhhhh......ee...........hhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhh.......eee..hhhhhh........ee........hhhhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5x0y O  670 LLDQTKDTRITHLLRQTNAFLDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNHLNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTISFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSKLSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQMLKYRRLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRVAGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSELLRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNEVRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERRKKREELKDSEINEILARNDEEMAVLTRMDEDRSKKEEKSRLLEKKREESESAAVYNGR 1349
                                   679       689||     751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       967       977       987       997      1007      1017      1027    ||1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1277      1287      1297      1307 ||   1336      1346   
                                              690|                                                                                                                                                                                                                      960|                                                             1032|                                                                                                                                                                                                                           1269|                            1309|  1320|             
                                               743                                                                                                                                                                                                                       967                                                              1046                                                                                                                                                                                                                            1277                             1314   1336
   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 5X0Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X0Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X0Y)

(-) Gene Ontology  (36, 55)

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  5x0y
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  H2B11_XENLA | P02281
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  H32_XENLA | P84233
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  H4_XENLA | P62799
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  Q6AZJ8_XENLA | Q6AZJ8
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  SNF2_YEAST | P22082
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 Related Entries

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

UniProtKB/Swiss-Prot
        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 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5hq2 5nl0 5x0x
        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 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x
        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 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x
        Q6AZJ8_XENLA | Q6AZJ8: 2nzd 3b6f 3b6g 3kuy 3kwq 3lja 3mnn 3tu4 3ut9 3uta 3utb 4j8v 4j8w 4j8x 4ld9 4xuj 4xzq 4ys3 4z66 5cp6 5dnm 5dnn 5e5a 5hq2
        SNF2_YEAST | P22082: 4i6m 5x0x
UniProtKB/TrEMBL
        Q6AZJ8_XENLA | Q6AZJ8: 3kxb 3lel 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mvd 4kgc 4kha 4r8p 5x0x

(-) Related Entries Specified in the PDB File

5x0x RELATED ID: EMD-6699 RELATED DB: EMDB