4YS3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   NUCLEOSOME DISASSEMBLY BY RSC AND SWI/SNF IS ENHANCED BY H3 ACETYLATION NEAR THE NUCLEOSOME DYAD AXIS

Authors :   M. L. Dechassa, K. Luger, N. Chatterjee, J. A. North, M. Manohar, R. Pras J. J. Ottessen, M. G. Poirier, B. Bartholomew

Date :   16 Mar 15 (Deposition) - 14 Oct 15 (Release) - 11 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H,I,J

Keywords :   Dyad Axis, Structural Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Chatterjee, J. A. North, M. L. Dechassa, M. Manohar, R. Prasad, K. Luger, J. J. Ottesen, M. G. Poirier, B. Bartholomew
Histone Acetylation Near The Nucleosome Dyad Axis Enhances Nucleosome Disassembly By Rsc And Swi/Snf.
Mol. Cell. Biol. V. 35 4083 2015
PubMed-ID: 26416878 | Reference-DOI: 10.1128/MCB.00441-15

Molecule 1 - HISTONE H3.2
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 39-136
	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
	Fragment	:	RESIDUES 25-103
	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
	Fragment	:	RESIDUES 15-121
	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
	Fragment	:	RESIDUES 34-126
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	H2B1.1

Molecule 5 - DNA (147-MER)
	Chains	:	I
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

Molecule 6 - DNA (147-MER)
	Chains	:	J
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ALY	4	Mod. Amino Acid	N(6)-ACETYLLYSINE

(no "Site" information available for 4YS3)

(no "SS Bond" information available for 4YS3)

(no "Cis Peptide Bond" information available for 4YS3)

(no "SAP(SNP)/Variant" information available for 4YS3)

(no "PROSITE Motif" information available for 4YS3)

(no "Exon" information available for 4YS3)

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.......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                4ys3 A  438 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAkRVTIMPkDIQLARRIRGERA  535
                                   447       457       467       477       487       497       507       517    |  527        
                                                                                                       515-ALY  |             
                                                                                                              522-ALY

Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                                
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                4ys3 B   24 DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  102
                                    33        43        53        63        73        83        93

Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                4ys3 C  814 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT  920
                                   823       833       843       853       863       873       883       893       903       913

Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                4ys3 D 1230 RKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 1322
                                  1239      1249      1259      1269      1279      1289      1299      1309      1319

Chain E from PDB  Type:PROTEIN  Length:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                4ys3 E  638 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAkRVTIMPkDIQLARRIRGERA  735
                                   647       657       667       677       687       697       707       717    |  727        
                                                                                                       715-ALY  |             
                                                                                                              722-ALY

Chain F from PDB  Type:PROTEIN  Length:79
                                                                                                                
               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
                4ys3 F  224 DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  302
                                   233       243       253       263       273       283       293

Chain G from PDB  Type:PROTEIN  Length:106
                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                4ys3 G 1014 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 1119
                                  1023      1033      1043      1053      1063      1073      1083      1093      1103      1113

Chain H from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                4ys3 H 1430 RKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 1522
                                  1439      1449      1459      1469      1479      1489      1499      1509      1519

Chain I from PDB  Type:DNA  Length:147
                                                                                                                                                                                    
                4ys3 I    1 ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT  147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain J from PDB  Type:DNA  Length:147
                                                                                                                                                                                    
                4ys3 J  148 ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT  294
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287

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 '\|'

(no "SCOP Domain" information available for 4YS3)

(no "CATH Domain" information available for 4YS3)

(no "Pfam Domain" information available for 4YS3)

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Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 4ys3)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ys3)

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (9, 30)

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