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Asym./Biol. Unit (Jmol Viewer)

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

Title :   MONOCLINIC COMPLEX STRUCTURE OF ATRX ADD BOUND TO HISTONE H3K9ME3 PEPTIDE

Authors :   B. Xiang, H. Li

Date :   02 Feb 11 (Deposition) - 15 Jun 11 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.93

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

Keywords :   Zinc Finger, Transcription, Histone, Lysine Trimethylation, Nuclear Protein, Histone-Binding Protein, Transcription-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Iwase, B. Xiang, S. Ghosh, T. Ren, P. W. Lewis, J. C. Cochrane, C. D. Allis, D. J. Picketts, D. J. Patel, H. Li, Y. Shi
Atrx Add Domain Links An Atypical Histone Methylation Recognition Mechanism To Human Mental-Retardation Syndrome
Nat. Struct. Mol. Biol. V. 18 769 2011
PubMed-ID: 21666679 | Reference-DOI: 10.1038/NSMB.2062

Molecule 1 - TRANSCRIPTIONAL REGULATOR ATRX
	Chains	:	A
	EC Number	:	3.6.4.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL ADD DOMAIN, UNP RESIDUES 167-289
	Gene	:	ATRX, RAD54L, XH2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED NUCLEAR PROTEIN, XNP, ZNF-HX

Molecule 2 - PEPTIDE OF HISTONE H3.3
	Chains	:	C
	Engineered	:	YES
	Fragment	:	K9 TRIMETHYLATED H3 N-TERMINAL FRAGMENT, UNP RESIDUES 2-16
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:171 , CYS A:174 , CYS A:197 , CYS A:200	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	CYS A:220 , CYS A:223 , CYS A:240 , CYS A:243	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	CYS A:232 , CYS A:235 , CYS A:265 , CYS A:268	BINDING SITE FOR RESIDUE ZN A 3

(no "SS Bond" information available for 3QL9)

(no "Cis Peptide Bond" information available for 3QL9)

Asymmetric/Biological Unit (17, 17)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_012113	G	175	E	ATRX_HUMAN	Disease (ATRX)	---	A	G	175	E
02	UniProt	VAR_012115	N	179	S	ATRX_HUMAN	Disease (ATRX)	---	A	N	179	S
03	UniProt	VAR_001226	P	190	A	ATRX_HUMAN	Disease (ATRX)	---	A	P	190	A
04	UniProt	VAR_012116	P	190	L	ATRX_HUMAN	Disease (ATRX)	---	A	P	190	L
05	UniProt	VAR_012117	P	190	S	ATRX_HUMAN	Disease (ATRX)	---	A	P	190	S
06	UniProt	VAR_001227	L	192	F	ATRX_HUMAN	Disease (ATRX)	---	A	L	192	F
07	UniProt	VAR_012118	V	194	I	ATRX_HUMAN	Disease (ATRX)	---	A	V	194	I
08	UniProt	VAR_001228	C	200	S	ATRX_HUMAN	Disease (ATRX)	---	A	C	200	S
09	UniProt	VAR_012119	Q	219	P	ATRX_HUMAN	Disease (ATRX)	---	A	Q	219	P
10	UniProt	VAR_001229	C	220	R	ATRX_HUMAN	Disease (ATRX)	---	A	C	220	R
11	UniProt	VAR_032625	C	220	Y	ATRX_HUMAN	Disease (MRXSHF1)	---	A	C	220	Y
12	UniProt	VAR_001230	W	222	S	ATRX_HUMAN	Disease (ATRX)	---	A	W	222	S
13	UniProt	VAR_001231	C	243	F	ATRX_HUMAN	Disease (ATRX)	---	A	C	243	F
14	UniProt	VAR_001232	R	246	C	ATRX_HUMAN	Disease (ATRX)	---	A	R	246	C
15	UniProt	VAR_010914	R	246	L	ATRX_HUMAN	Disease (ATRX)	---	A	R	246	L
16	UniProt	VAR_012120	G	249	C	ATRX_HUMAN	Disease (ATRX)	---	A	G	249	C
17	UniProt	VAR_001233	G	249	D	ATRX_HUMAN	Disease (ATRX)	---	A	G	249	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3QL9)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000366816	1	ENSE00001442675	chr1:226249552-226249795	244	H33_HUMAN	-	0	0	-	-
1.2c	ENST00000366816	2c	ENSE00001442674	chr1:226250436-226250512	77	H33_HUMAN	-	0	0	-	-
1.3b	ENST00000366816	3b	ENSE00001428176	chr1:226252030-226252180	151	H33_HUMAN	1-43	43	1	C:1-10	10
1.4a	ENST00000366816	4a	ENSE00001692850	chr1:226253357-226253510	154	H33_HUMAN	43-94	52	0	-	-
1.5a	ENST00000366816	5a	ENSE00001381318	chr1:226259052-226259224	173	H33_HUMAN	95-136	42	0	-	-

2.1a	ENST00000373344	1a	ENSE00002167359	X:77041702-77041468	235	ATRX_HUMAN	1-7	7	0	-	-
2.2	ENST00000373344	2	ENSE00001636919	X:76972720-76972608	113	ATRX_HUMAN	7-45	39	0	-	-
2.4b	ENST00000373344	4b	ENSE00001688675	X:76954117-76954062	56	ATRX_HUMAN	45-63	19	0	-	-
2.5	ENST00000373344	5	ENSE00001763951	X:76953123-76953071	53	ATRX_HUMAN	64-81	18	0	-	-
2.6	ENST00000373344	6	ENSE00001652735	X:76952192-76952065	128	ATRX_HUMAN	81-124	44	0	-	-
2.7a	ENST00000373344	7a	ENSE00002168990	X:76949426-76949313	114	ATRX_HUMAN	124-162	39	0	-	-
2.9	ENST00000373344	9	ENSE00002165776	X:76944420-76944311	110	ATRX_HUMAN	162-198	37	1	A:165-198	34
2.10	ENST00000373344	10	ENSE00001694382	X:76940498-76940431	68	ATRX_HUMAN	199-221	23	1	A:199-221	23
2.11b	ENST00000373344	11b	ENSE00002071055	X:76940085-76937012	3074	ATRX_HUMAN	221-1246	1026	1	A:221-289	69
2.12a	ENST00000373344	12a	ENSE00001638399	X:76931793-76931721	73	ATRX_HUMAN	1246-1270	25	0	-	-
2.13	ENST00000373344	13	ENSE00001655114	X:76920267-76920134	134	ATRX_HUMAN	1270-1315	46	0	-	-
2.14	ENST00000373344	14	ENSE00001618412	X:76919047-76918871	177	ATRX_HUMAN	1315-1374	60	0	-	-
2.15	ENST00000373344	15	ENSE00001759922	X:76912143-76912050	94	ATRX_HUMAN	1374-1405	32	0	-	-
2.16	ENST00000373344	16	ENSE00002155398	X:76909690-76909588	103	ATRX_HUMAN	1405-1439	35	0	-	-
2.17	ENST00000373344	17	ENSE00001804555	X:76907843-76907604	240	ATRX_HUMAN	1440-1519	80	0	-	-
2.18	ENST00000373344	18	ENSE00001692523	X:76891547-76891406	142	ATRX_HUMAN	1520-1567	48	0	-	-
2.19a	ENST00000373344	19a	ENSE00001634558	X:76890194-76890085	110	ATRX_HUMAN	1567-1603	37	0	-	-
2.20a	ENST00000373344	20a	ENSE00001729307	X:76889200-76889054	147	ATRX_HUMAN	1604-1652	49	0	-	-
2.21	ENST00000373344	21	ENSE00001679104	X:76888872-76888695	178	ATRX_HUMAN	1653-1712	60	0	-	-
2.22	ENST00000373344	22	ENSE00001611054	X:76876000-76875863	138	ATRX_HUMAN	1712-1758	47	0	-	-
2.23	ENST00000373344	23	ENSE00001600235	X:76874449-76874274	176	ATRX_HUMAN	1758-1816	59	0	-	-
2.24	ENST00000373344	24	ENSE00001614801	X:76872198-76872081	118	ATRX_HUMAN	1817-1856	40	0	-	-
2.26b	ENST00000373344	26b	ENSE00001611019	X:76856033-76855903	131	ATRX_HUMAN	1856-1899	44	0	-	-
2.27b	ENST00000373344	27b	ENSE00001762228	X:76855289-76855201	89	ATRX_HUMAN	1900-1929	30	0	-	-
2.28	ENST00000373344	28	ENSE00001627804	X:76855049-76854880	170	ATRX_HUMAN	1929-1986	58	0	-	-
2.29	ENST00000373344	29	ENSE00001690714	X:76849319-76849166	154	ATRX_HUMAN	1986-2037	52	0	-	-
2.30	ENST00000373344	30	ENSE00001637691	X:76845410-76845304	107	ATRX_HUMAN	2037-2073	37	0	-	-
2.31	ENST00000373344	31	ENSE00001632927	X:76829823-76829715	109	ATRX_HUMAN	2073-2109	37	0	-	-
2.32	ENST00000373344	32	ENSE00001674842	X:76814317-76814140	178	ATRX_HUMAN	2109-2168	60	0	-	-
2.33	ENST00000373344	33	ENSE00001762255	X:76813116-76812922	195	ATRX_HUMAN	2169-2233	65	0	-	-
2.34	ENST00000373344	34	ENSE00001605899	X:76778879-76778730	150	ATRX_HUMAN	2234-2283	50	0	-	-
2.35	ENST00000373344	35	ENSE00001640278	X:76777866-76777741	126	ATRX_HUMAN	2284-2325	42	0	-	-
2.36	ENST00000373344	36	ENSE00001609746	X:76776976-76776881	96	ATRX_HUMAN	2326-2357	32	0	-	-
2.37	ENST00000373344	37	ENSE00001620267	X:76776394-76776266	129	ATRX_HUMAN	2358-2400	43	0	-	-
2.38	ENST00000373344	38	ENSE00001885562	X:76764107-76760378	3730	ATRX_HUMAN	2401-2492	92	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
	(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:125
 aligned with ATRX_HUMAN | P46100 from UniProtKB/Swiss-Prot  Length:2492

    Alignment length:125
                                   174       184       194       204       214       224       234       244       254       264       274       284     
           ATRX_HUMAN   165 LHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQ 289
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eee......eeehhhhhhhhhh....................eeee......eeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ----------E---S----------A-F-I-----S------------------PR-S--------------------F--C--C---------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------L-----------------------------Y-------------------------L--D---------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------S--------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.9  PDB: A:165-198          Exon 2.10              -------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) --------------------------------------------------------Exon 2.11b  PDB: A:221-289 UniProt: 221-1246 [INCOMPLETE]             Transcript 2 (2)
                 3ql9 A 165 SMGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYENLEQ 289
                                   174       184       194       204       214       224       234       244       254       264       274       284

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    11
            H33_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..eee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.3b  Transcript 1
                 3ql9 C   1 ARTKQTARkS  10
                                    10
                                    9-M3L

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3QL9)

(no "CATH Domain" information available for 3QL9)

(no "Pfam Domain" information available for 3QL9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ATRX_HUMAN | P46100)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003678	DNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
	GO:0015616	DNA translocase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0070087	chromo shadow domain binding	Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0030330	DNA damage response, signal transduction by p53 class mediator	A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	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:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0060009	Sertoli cell development	The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate.
	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:0072711	cellular response to hydroxyurea	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 hydroxyurea stimulus.
	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:0030900	forebrain development	The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:1904908	negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric	Any process that stops, prevents or reduces the frequency, rate or extent of maintenance of mitotic sister chromatid cohesion, telomeric.
	GO:1901581	negative regulation of telomeric RNA transcription from RNA pol II promoter	Any process that stops, prevents or reduces the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
	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:0010571	positive regulation of nuclear cell cycle DNA replication	Any process that activates or increases the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.
	GO:0032206	positive regulation of telomere maintenance	Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
	GO:1901582	positive regulation of telomeric RNA transcription from RNA pol II promoter	Any process that activates or increases the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
	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.
	GO:0035128	post-embryonic forelimb morphogenesis	The process, occurring after embryonic development, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an organism.
	GO:0070198	protein localization to chromosome, telomeric region	Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0031297	replication fork processing	The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
	GO:0072520	seminiferous tubule development	The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0070603	SWI/SNF superfamily-type complex	A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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:1990707	nuclear subtelomeric heterochromatin	Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
	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:0005721	pericentric heterochromatin	Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:0031933	telomeric heterochromatin	Heterochromatic regions of the chromosome found at the telomeres.

Chain C (H33_HUMAN | P84243)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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: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:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	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:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
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: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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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Description

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Ligands, Modified Residues, Ions (2, 4)

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