2BYK - JenaLib

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Title :   HISTONE FOLD HETERODIMER OF THE CHROMATIN ACCESSIBILITY COMPLEX

Authors :   C. Fernandez-Tornero, K. F. Hartlepp, T. Grune, A. Eberharter, P. B. Becker, C. W. Muller

Date :   03 Aug 05 (Deposition) - 09 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Chrac-14, Nucleosome Sliding, Histone Fold, Chrac-16, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. F. Hartlepp, C. Fernandez-Tornero, A. Eberharter, T. Grune, C. W. Muller, P. B. Becker
The Histone Fold Subunits Of Drosophila Chrac Facilitate Nucleosome Sliding Through Dynamic Dna Interactions.
Mol. Cell. Biol. V. 25 9886 2005
PubMed-ID: 16260604 | Reference-DOI: 10.1128/MCB.25.22.9886-9896.2005

Molecule 1 - CHRAC-14
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T-CHRAC14/16
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	RE59557P, CG15736-PA

Molecule 2 - CHRAC-16
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T-CHRAC14/16
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	CG32956-PA ISOFORM A, CG32956-PE, ISOFORM E

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:97 , GLN A:98 , LYS A:99 , ARG C:69 , GLU C:72	BINDING SITE FOR RESIDUE SO4 A2101
2	AC2	SOFTWARE	LYS A:75 , TYR A:76 , HOH A:2010 , SER B:30 , GLU B:32	BINDING SITE FOR RESIDUE SO4 B3100
3	AC3	SOFTWARE	LYS C:75 , TYR C:76 , SER D:30 , GLU D:32	BINDING SITE FOR RESIDUE SO4 D5099

(no "SS Bond" information available for 2BYK)

(no "Cis Peptide Bond" information available for 2BYK)

(no "SAP(SNP)/Variant" information available for 2BYK)

(no "PROSITE Motif" information available for 2BYK)

(no "Exon" information available for 2BYK)

Asymmetric 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:72
 aligned with Q9V452_DROME | Q9V452 from UniProtKB/TrEMBL  Length:140

    Alignment length:72
                                    38        48        58        68        78        88        98  
         Q9V452_DROME    29 MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKI 100
               SCOP domains d2byka1 A:29-100 Chrac-16                                                SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2byk A  29 MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKI 100
                                    38        48        58        68        78        88        98

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with Q9V444_DROME | Q9V444 from UniProtKB/TrEMBL  Length:128

    Alignment length:89
                                    20        30        40        50        60        70        80        90         
         Q9V444_DROME    11 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEK  99
               SCOP domains d2bykb1 B:11-99 Chrac-14                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2byk B  11 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEK  99
                                    20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:66
 aligned with Q9V452_DROME | Q9V452 from UniProtKB/TrEMBL  Length:140

    Alignment length:66
                                    42        52        62        72        82        92      
         Q9V452_DROME    33 MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQ  98
               SCOP domains d2bykc_ C: Chrac-16                                                SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2byk C  33 MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQ  98
                                    42        52        62        72        82        92

Chain D from PDB  Type:PROTEIN  Length:92
 aligned with Q9V444_DROME | Q9V444 from UniProtKB/TrEMBL  Length:128

    Alignment length:92
                                    16        26        36        46        56        66        76        86        96  
         Q9V444_DROME     7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKE  98
               SCOP domains d2bykd_ D: Chrac-14                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2byk D   7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKE  98
                                    16        26        36        46        56        66        76        86        96

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Histone-fold (277)

Superfamily: Histone-fold (277)

Family: TBP-associated factors, TAFs (19)

Protein domain: Chrac-14 (2)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (2)

1a	d2bykb1	B:11-99
1b	d2bykd_	D:

Protein domain: Chrac-16 (2)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (2)

2a	d2byka1	A:29-100
2b	d2bykc_	C:

(no "CATH Domain" information available for 2BYK)

(no "Pfam Domain" information available for 2BYK)

Asymmetric Unit(hide GO term definitions)

Chain A,C (Q9V452_DROME | Q9V452)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0070615	nucleosome-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of one or more nucleosomes.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0042766	nucleosome mobilization	The movement of nucleosomes along a DNA fragment.
cellular component
	GO:0008623	CHRAC	An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and additional small histone fold subunits (generally two of these, but Xenopus has only one and some additional non-conserved subunits). CHRAC plays roles in the regulation of RNA polymerase II transcription and in DNA replication and repair.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B,D (Q9V444_DROME | Q9V444)

molecular function
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	GO:0070615	nucleosome-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of one or more nucleosomes.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0034080	CENP-A containing nucleosome assembly	The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0071480	cellular response to gamma radiation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0042766	nucleosome mobilization	The movement of nucleosomes along a DNA fragment.
cellular component
	GO:0005671	Ada2/Gcn5/Ada3 transcription activator complex	A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
	GO:0008623	CHRAC	An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and additional small histone fold subunits (generally two of these, but Xenopus has only one and some additional non-conserved subunits). CHRAC plays roles in the regulation of RNA polymerase II transcription and in DNA replication and repair.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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2bym	HISTONE FOLD HETERODIMER OF THE CHROMATIN ACCESSIBILITY COMPLEX

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

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