2HUE - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF THE H3-H4 CHAPERONE ASF1 BOUND TO HISTONES H3 AND H4

Authors :   C. M English, M. E. A. Churchill, J. K. Tyler

Date :   26 Jul 06 (Deposition) - 21 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (2x)
Biol. Unit 3: A (2x),B (2x),C (2x)
Biol. Unit 4: A (2x),B (2x),C (2x)

Keywords :   Mini Beta Sheet, Elongated Beta Sandwhich, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. English, M. W. Adkins, J. J. Carson, M. E. Churchill, J. K. Tyler
Structural Basis For The Histone Chaperone Activity Of Asf1
Cell(Cambridge, Mass. ) V. 127 495 2006
PubMed-ID: 17081973 | Reference-DOI: 10.1016/J.CELL.2006.08.047

Molecule 1 - ANTI-SILENCING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PST39
	Expression System Strain	:	ROSETTA DE3 PLYS S
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-169
	Gene	:	ASF1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - HISTONE H3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PST39
	Expression System Strain	:	ROSETTA DE3 PLYS S
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 62-136
	Gene	:	H3L
	Mutation	:	YES
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 3 - HISTONE H4
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PST39
	Expression System Strain	:	ROSETTA DE3 PLYS S
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 20-102
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:63 , HOH B:426 , HOH B:434 , HOH B:455 , HOH B:467 , HOH B:472 , THR C:30 , PRO C:32 , ARG C:36	BINDING SITE FOR RESIDUE SO4 B 401
2	AC2	SOFTWARE	SER A:91 , VAL A:92 , GOL A:501 , HOH A:568 , ARG B:116 , LYS B:122 , HOH B:439 , HOH B:474	BINDING SITE FOR RESIDUE SO4 B 402
3	AC3	SOFTWARE	ASP A:133 , HIS A:134 , HOH A:558	BINDING SITE FOR RESIDUE ZN A 403
4	AC4	SOFTWARE	VAL A:90 , SER A:91 , ASN A:114 , ASN A:115 , GLU A:116 , HOH A:568 , ALA B:114 , LYS B:115 , SO4 B:402 , HOH B:439	BINDING SITE FOR RESIDUE GOL A 501
5	AC5	SOFTWARE	GLU B:73 , ASP B:77 , ARG C:23 , ILE C:26 , LYS C:59 , HOH C:512	BINDING SITE FOR RESIDUE GOL C 502

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

Asymmetric Unit

No.	Residues
1	Asn A:14	-	Pro A:15
2	Gly A:63	-	Pro A:64

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H32_XENLA	67-75	1	B:66-74

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H32_XENLA	67-75	1	B:66-74

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H32_XENLA	67-75	2	B:66-74

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H32_XENLA	67-75	2	B:66-74

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H32_XENLA	67-75	2	B:66-74

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJL115W	1	YJL115W.1	X:196284-197123	840	ASF1_YEAST	1-279	279	1	A:1-164	164

Asymmetric Unit

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	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:164
 aligned with ASF1_YEAST | P32447 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ASF1_YEAST     1 MSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPP 164
               SCOP domains -d2huea1 A:2-164 Anti-silencing protein 1, ASF1                                                                                                                      SCOP domains
               CATH domains 2hueA00 A:1-164 ASF1-like                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....ee....eeeeeeeee.......eeeeeeee....hhh.eeeeeeeee.....eeeeeeeee...hhhhhhhhhhh..eeeeeeeee..eeeeeeeeeeeeee.hhhhhhh.....hhh.eeeee.....eeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-164 UniProt: 1-279 [INCOMPLETE]                                                                                                                   Transcript 1
                 2hue A   1 SSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPP 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with H32_XENLA | P84233 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:75
                                    70        80        90       100       110       120       130     
            H32_XENLA    61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
               SCOP domains d2hueb_ B: automated matches                                                SCOP domains
               CATH domains 2hueB00 B:60-134 Histone, subunit A                                         CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE_H------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2hue B  60 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:75
                                    70        80        90       100       110       120       130     
         Q92133_XENLA    61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCGIHAKRVTIMPKDIQLARRIRGER 135
               SCOP domains d2hueb_ B: automated matches                                                SCOP domains
               CATH domains 2hueB00 B:60-134 Histone, subunit A                                         CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2hue B  60 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    69        79        89        99       109       119       129

Chain C from PDB  Type:PROTEIN  Length:82
 aligned with H4_XENLA | P62799 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:82
                                    30        40        50        60        70        80        90       100  
             H4_XENLA    21 KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG 102
               SCOP domains d2huec_ C: Histone H4                                                              SCOP domains
               CATH domains 2hueC00 C:20-101 Histone, subunit A                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2hue C  20 KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG 101
                                    29        39        49        59        69        79        89        99

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Histone, subunit A (62)

Homologous Superfamily: Histone, subunit A (62)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	2hueC00	C:20-101
1b	2hueB00	B:60-134

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: ASF1-like (13)

Baker's yeast (Saccharomyces cerevisiae) (4)

2hueA00

A:1-164

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

Asymmetric Unit(hide GO term definitions)

Chain A (ASF1_YEAST | P32447)

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: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).
biological process
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0006348	chromatin silencing at telomere	Repression of transcription of telomeric DNA by altering the structure of chromatin.
	GO:0033523	histone H2B ubiquitination	The modification of histone H2B by addition of ubiquitin groups.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0043486	histone exchange	The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits.
	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.
	GO:0006337	nucleosome disassembly	The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0035066	positive regulation of histone acetylation	Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0043618	regulation of transcription from RNA polymerase II promoter in response to stress	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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 (H32_XENLA | P84233)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
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: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 B (Q92133_XENLA | Q92133)

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.
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: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 (H4_XENLA | P62799)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	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: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.

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	Q92133_XENLA \| Q92133
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1kx5	X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION
1roc	CRYSTAL STRUCTURE OF THE HISTONE DEPOSITION PROTEIN ASF1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (27, 41)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File