1ID3 | PD0209 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

Authors :   C. L. White, R. K. Suto, K. Luger

Date :   03 Apr 01 (Deposition) - 28 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Nucleosome Core Particle, Chromatin, Histone, Protein/Dna Interaction, Nucleoprotein, Supercoiled Dna, Complex (Nucleosome Core/Dna), Structural Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. White, R. K. Suto, K. Luger
Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Changes In Internucleosome Interactions.
Embo J. V. 20 5207 2001
PubMed-ID: 11566884 | Reference-DOI: 10.1093/EMBOJ/20.18.5207
(for further references see the PDB file header)

Molecule 1 - PALINDROMIC 146BP DNA FRAGMENT
	Chains	:	I, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ALPHA SAT DNA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HISTONE H3
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HISTONE H3
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 3 - HISTONE H4
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HISTONE H4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 4 - HISTONE H2A.1
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HISTONE H2A
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 5 - HISTONE H2B.2
	Chains	:	D, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 DE3 PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HISTONE H2B
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		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, 17)

No.	Name	Count	Type	Full Name
1	MN	17	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY G:45 , SER G:46 , GLY G:47 , SER H:93 , ALA H:94	BINDING SITE FOR RESIDUE MN H 131
02	AC2	SOFTWARE	ARG C:89	BINDING SITE FOR RESIDUE MN C 132
03	AC3	SOFTWARE	DG J:267	BINDING SITE FOR RESIDUE MN J 103
04	AC4	SOFTWARE	DA I:133 , DG I:134	BINDING SITE FOR RESIDUE MN I 147
05	AC5	SOFTWARE	DG I:70	BINDING SITE FOR RESIDUE MN I 148
06	AC6	SOFTWARE	ASP G:91 , GLU G:93	BINDING SITE FOR RESIDUE MN G 132
07	AC7	SOFTWARE	DG I:121	BINDING SITE FOR RESIDUE MN I 149
08	AC8	SOFTWARE	DA J:279 , DG J:280	BINDING SITE FOR RESIDUE MN J 108
09	AC9	SOFTWARE	ARG E:49 , DT I:8	BINDING SITE FOR RESIDUE MN E 136
10	BC1	SOFTWARE	ASP C:91 , GLU C:93	BINDING SITE FOR RESIDUE MN C 133
11	BC2	SOFTWARE	DG J:216 , DG J:217	BINDING SITE FOR RESIDUE MN J 111
12	BC3	SOFTWARE	DG I:78 , DG J:214	BINDING SITE FOR RESIDUE MN I 150
13	BC4	SOFTWARE	ASP C:73 , DC J:168	BINDING SITE FOR RESIDUE MN J 113
14	BC5	SOFTWARE	DT I:45 , DG J:246	BINDING SITE FOR RESIDUE MN J 114
15	BC6	SOFTWARE	DT J:184 , DG J:185 , DG J:186	BINDING SITE FOR RESIDUE MN J 115
16	BC7	SOFTWARE	GLU D:108 , HIS D:112 , GLU G:65 , HIS H:52	BINDING SITE FOR RESIDUE MN D 131
17	BC8	SOFTWARE	DA J:202 , DA J:203	BINDING SITE FOR RESIDUE MN J 117

(no "SS Bond" information available for 1ID3)

(no "Cis Peptide Bond" information available for 1ID3)

(no "SAP(SNP)/Variant" information available for 1ID3)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H2A	PS00046	Histone H2A signature.	H2A1_YEAST	23-29	2	C:22-28 G:22-28
2	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H3_YEAST	67-75	2	A:66-74 E:66-74
3	HISTONE_H2B	PS00357	Histone H2B signature.	H2B2_YEAST	96-118	2	D:95-117 H:95-117

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBL002W	1	YBL002W.1	II:236495-236890	396	H2B2_YEAST	1-131	131	2	D:36-128 H:35-130	93 96

2.1	YDR225W	1	YDR225W.1	IV:915527-915925	399	H2A1_YEAST	1-132	132	2	C:16-125 G:13-120	110 108

3.1	YNL030W	1	YNL030W.1	XIV:576729-577040	312	H4_YEAST	1-103	103	2	B:24-102 F:18-102	79 85

4.1	YNL031C	1	YNL031C.1	XIV:576052-575642	411	H3_YEAST	1-136	136	2	A:38-134 E:38-134	97 97

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:97
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:97
                                    48        58        68        78        88        98       108       118       128       
             H3_YEAST    39 PHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGER 135
               SCOP domains d1id3a_ A: Histone H3                                                                             SCOP domains
               CATH domains 1id3A00 A:38-134 Histone, subunit A                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HISTONE_H------------------------------------------------------------ PROSITE
               Transcript 4 Exon 4.1  PDB: A:38-134 UniProt: 1-136 [INCOMPLETE]                                               Transcript 4
                 1id3 A  38 PHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKEIKLARRLRGER 134
                                    47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:79
                                    34        44        54        64        74        84        94         
             H4_YEAST    25 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 103
               SCOP domains d1id3b_ B: Histone H4                                                           SCOP domains
               CATH domains 1id3B00 B:24-102 Histone, subunit A                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: B:24-102 UniProt: 1-103 [INCOMPLETE]                             Transcript 3
                 1id3 B  24 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 102
                                    33        43        53        63        73        83        93

Chain C from PDB  Type:PROTEIN  Length:110
 aligned with H2A1_YEAST | P04911 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:110
                                    26        36        46        56        66        76        86        96       106       116       126
           H2A1_YEAST    17 QSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKSAKAT 126
               SCOP domains d1id3c_ C: Histone H2A                                                                                         SCOP domains
               CATH domains 1id3C00 C:16-125 Histone, subunit A                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: C:16-125 UniProt: 1-132 [INCOMPLETE]                                                            Transcript 2
                 1id3 C  16 QSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKSAKAT 125
                                    25        35        45        55        65        75        85        95       105       115       125

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with H2B2_YEAST | P02294 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:93
                                    46        56        66        76        86        96       106       116       126   
           H2B2_YEAST    37 RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSST 129
               SCOP domains d1id3d_ D: Histone H2B                                                                        SCOP domains
               CATH domains 1id3D00 D:36-128 Histone, subunit A                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------HISTONE_H2B            ----------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:36-128 UniProt: 1-131 [INCOMPLETE]                                           Transcript 1
                 1id3 D  36 RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSST 128
                                    45        55        65        75        85        95       105       115       125

Chain E from PDB  Type:PROTEIN  Length:97
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:97
                                    48        58        68        78        88        98       108       118       128       
             H3_YEAST    39 PHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGER 135
               SCOP domains d1id3e_ E: Histone H3                                                                             SCOP domains
               CATH domains 1id3E00 E:38-134 Histone, subunit A                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HISTONE_H------------------------------------------------------------ PROSITE
               Transcript 4 Exon 4.1  PDB: E:38-134 UniProt: 1-136 [INCOMPLETE]                                               Transcript 4
                 1id3 E  38 PHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKEIKLARRLRGER 134
                                    47        57        67        77        87        97       107       117       127

Chain F from PDB  Type:PROTEIN  Length:85
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:85
                                    28        38        48        58        68        78        88        98     
             H4_YEAST    19 HRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 103
               SCOP domains d1id3f_ F: Histone H4                                                                 SCOP domains
               CATH domains 1id3F00 F:18-102 Histone, subunit A                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: F:18-102 UniProt: 1-103 [INCOMPLETE]                                   Transcript 3
                 1id3 F  18 HRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 102
                                    27        37        47        57        67        77        87        97

Chain G from PDB  Type:PROTEIN  Length:108
 aligned with H2A1_YEAST | P04911 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:108
                                    23        33        43        53        63        73        83        93       103       113        
           H2A1_YEAST    14 KASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK 121
               SCOP domains d1id3g_ G: Histone H2A                                                                                       SCOP domains
               CATH domains 1id3G00 G:13-120 Histone, subunit A                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh....hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------HISTONE-------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: G:13-120 UniProt: 1-132 [INCOMPLETE]                                                          Transcript 2
                 1id3 G  13 KASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK 120
                                    22        32        42        52        62        72        82        92       102       112

Chain H from PDB  Type:PROTEIN  Length:96
 aligned with H2B2_YEAST | P02294 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:96
                                    45        55        65        75        85        95       105       115       125      
           H2B2_YEAST    36 VRKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSSTQA 131
               SCOP domains d1id3h_ H: Histone H2B                                                                           SCOP domains
               CATH domains 1id3H00 H:35-130 Histone, subunit A                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------HISTONE_H2B            ------------- PROSITE
               Transcript 1 Exon 1.1  PDB: H:35-130 UniProt: 1-131 [INCOMPLETE]                                              Transcript 1
                 1id3 H  35 VRKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSSSTQA 130
                                    44        54        64        74        84        94       104       114       124

Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 1id3 I   1 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 1id3 J 147 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 292
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286

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/Biological 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)

Human (Homo sapiens) (28)

1a	1id3A00	A:38-134
1b	1id3G00	G:13-120
1c	1id3C00	C:16-125
1d	1id3F00	F:18-102
1e	1id3B00	B:24-102
1f	1id3E00	E:38-134
1g	1id3H00	H:35-130
1h	1id3D00	D:36-128

(no "Pfam Domain" information available for 1ID3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,E (H3_YEAST | P61830)

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:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	GO:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0043505	CENP-A containing nucleosome	A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	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: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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Chain B,F (H4_YEAST | P02309)

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:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0034729	histone H3-K79 methylation	The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
	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:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0061587	transfer RNA gene-mediated silencing	The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
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: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: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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Chain C,G (H2A1_YEAST | P04911)

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:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	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:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0061587	transfer RNA gene-mediated silencing	The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
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: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: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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Chain D,H (H2B2_YEAST | P02294)

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:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	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: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: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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1id3)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1id3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	H2A1_YEAST \| P04911
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	H2B2_YEAST \| P02294
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	H3_YEAST \| P61830
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	H4_YEAST \| P02309
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	H2A1_YEAST \| P04911
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	H2B2_YEAST \| P02294
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	H3_YEAST \| P61830
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	H4_YEAST \| P02309
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1aoi	X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.8A
1eqz	X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5A RESOLUTION
1f66	2.6A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (4, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (19, 48)

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