4CAY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A HUMAN ANP32E-H2A.Z-H2B COMPLEX

Authors :   A. Obri, K. Ouararhni, C. Papin, M. -L. Diebold, K. Padmanabhan, M. Mare I. Stoll, L. Roy, P. T. Reilly, T. W. Mak, S. Dimitrov, C. Romier, A. Hami

Date :   09 Oct 13 (Deposition) - 22 Jan 14 (Release) - 14 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Epigenetics, Transcription, Nucleosome, Histone Variant, Histone Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Obri, K. Ouararhni, C. Papin, M. -L. Diebold, K. Padmanabhan, M. Marek, I. Stoll, L. Roy, P. T. Reilly, T. W. Wak, S. Dimitrov, C. Romier, A. Hamiche
Anp32E Is A Histone Chaperone That Removes H2A. Z From Chromatin
Nature V. 648 505 2014
PubMed-ID: 24463511 | Reference-DOI: 10.1038/NATURE12922

Molecule 1 - HISTONE H2A.Z
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNCS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	GLOBULAR DOMAIN, RESIDUES 19-128
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H2A/Z

Molecule 2 - HISTONE H2B TYPE 1-J
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNCS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	GLOBULAR DOMAIN, RESIDUES 31-126
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HISTONE H2B.1, HISTONE H2B.R, H2B/R, H2B

Molecule 3 - ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER E
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNEA-TH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	H2A.Z INTERACTING DOMAIN (ZID), RESIDUES 215-240
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LANP-LIKE PROTEIN, LANP-L, ANP32E

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 4CAY)

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

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

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H2A	PS00046	Histone H2A signature.	H2AZ_HUMAN	24-30	1	A:23-29
2	HISTONE_H2B	PS00357	Histone H2B signature.	H2B1J_HUMAN	93-115	1	B:92-114

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000296417	1a	ENSE00001134528	chr4:100871545-100871325	221	H2AZ_HUMAN	1-1	1	0	-	-
1.1g	ENST00000296417	1g	ENSE00001080673	chr4:100870897-100870820	78	H2AZ_HUMAN	2-27	26	1	A:18-26	9
1.1i	ENST00000296417	1i	ENSE00001780394	chr4:100870543-100870430	114	H2AZ_HUMAN	28-65	38	1	A:27-64 (gaps)	38
1.1k	ENST00000296417	1k	ENSE00001080674	chr4:100870097-100869968	130	H2AZ_HUMAN	66-109	44	1	A:65-107	43
1.1p	ENST00000296417	1p	ENSE00001080676	chr4:100869680-100869245	436	H2AZ_HUMAN	109-128	20	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:86
 aligned with H2AZ_HUMAN | P0C0S5 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:90
                                    28        38        48        58        68        78        88        98       108
           H2AZ_HUMAN    19 SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGG 108
               SCOP domains d4caya_ A: automated m    atches                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhhh----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----HISTONE------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1gExon 1.1i  PDB: A:27-64 (gaps)        Exon 1.1k  PDB: A:65-107 UniProt: 66-109    Transcript 1
                 4cay A  18 SRSQRAGLQFPVGRIHRHLKSR----GRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGG 107
                                    27        37 |    | 47        57        67        77        87        97       107
                                                39   44

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with H2B1J_HUMAN | P06899 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:92
                                    44        54        64        74        84        94       104       114       124  
          H2B1J_HUMAN    35 KESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 126
               SCOP domains d4cayb_ B: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4cay B  34 KESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125
                                    43        53        63        73        83        93       103       113       123

Chain C from PDB  Type:PROTEIN  Length:23
 aligned with AN32E_HUMAN | Q9BTT0 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:23
                                   224       234   
          AN32E_HUMAN   215 EVGLSYLMKEEIQDEEDDDDYVE 237
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 4cay C 215 EVGLSYLMKEEIQDEEDDDDYVE 237
                                   224       234

Legend:		→ Mismatch	(orange background)
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	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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Histone-fold (277)

Superfamily: Histone-fold (277)

Family: Nucleosome core histones (247)

Protein domain: automated matches (34)

Human (Homo sapiens) [TaxId: 9606] (25)

1a	d4caya_	A:
1b	d4cayb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (H2AZ_HUMAN | P0C0S5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
	GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	GO:0031492	nucleosomal DNA binding	Interacting selectively and non-covalently with the DNA portion of a nucleosome.
	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:0071392	cellular response to estradiol 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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
	GO:0001740	Barr body	A structure found in a female mammalian cell containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005719	nuclear euchromatin	The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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 (H2B1J_HUMAN | P06899)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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 C (AN32E_HUMAN | Q9BTT0)

molecular function
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0019212	phosphatase inhibitor activity	Stops, prevents or reduces the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule.
biological process
	GO:0043486	histone exchange	The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
cellular component
	GO:0000812	Swr1 complex	A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
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