2B2Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   TANDEM CHROMODOMAINS OF HUMAN CHD1

Authors :   J. F. Flanagan Iv, L. -Z. Mi, M. Chruszcz, M. Cymborowski, K. L. Clines, Y. Kim, W. Minor, F. Rastinejad, S. Khorasanizadeh

Date :   19 Sep 05 (Deposition) - 27 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Chd, Chromodomain, Three Stranded Antiparallel Beta Sheet, Alpha Helix Linker, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Flanagan, L. Z. Mi, M. Chruszcz, M. Cymborowski, K. L. Clines, Y. Kim, W. Minor, F. Rastinejad, S. Khorasanizadeh
Double Chromodomains Cooperate To Recognize The Methylated Histone H3 Tail.
Nature V. 438 1181 2005
PubMed-ID: 16372014 | Reference-DOI: 10.1038/NATURE04290
(for further references see the PDB file header)

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 268-443
	Gene	:	CHD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CHD-1

Molecule 2 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 268-373
	Gene	:	CHD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CHD-1

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2B2Y)

(no "Site" information available for 2B2Y)

(no "SS Bond" information available for 2B2Y)

Asymmetric/Biological Unit

No.	Residues
1	Glu C:54	-	Pro C:55

(no "SAP(SNP)/Variant" information available for 2B2Y)

Asymmetric/Biological Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CHD1_HUMAN	272-364 389-452	5	A:14-106 B:14-106 C:14-96 A:131-185 B:131-185
2	CHROMO_1	PS00598	Chromo domain signature.	CHD1_HUMAN	318-338 409-429	5	A:60-80 B:60-80 C:60-80 A:151-171 B:151-171

Asymmetric/Biological Unit (4, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000284049	1	ENSE00001083439	chr5:98262240-98262038	203	CHD1_HUMAN	1-18	18	0	-	-
1.2	ENST00000284049	2	ENSE00001013117	chr5:98240802-98240601	202	CHD1_HUMAN	18-85	68	0	-	-
1.3	ENST00000284049	3	ENSE00001013104	chr5:98239612-98239496	117	CHD1_HUMAN	86-124	39	0	-	-
1.4	ENST00000284049	4	ENSE00001013106	chr5:98238668-98238604	65	CHD1_HUMAN	125-146	22	0	-	-
1.5	ENST00000284049	5	ENSE00001013090	chr5:98237039-98236890	150	CHD1_HUMAN	146-196	51	0	-	-
1.6	ENST00000284049	6	ENSE00001013110	chr5:98236786-98236515	272	CHD1_HUMAN	196-287	92	3	A:12-29 B:11-29 C:11-29	18 19 19
1.7	ENST00000284049	7	ENSE00001013103	chr5:98235409-98235184	226	CHD1_HUMAN	287-362	76	3	A:29-104 (gaps) B:29-104 (gaps) C:29-96	76 76 68
1.8	ENST00000284049	8	ENSE00001013118	chr5:98234468-98234368	101	CHD1_HUMAN	362-396	35	2	A:104-138 B:104-138 -	35 35 -
1.9	ENST00000284049	9	ENSE00001013088	chr5:98234138-98233960	179	CHD1_HUMAN	396-455	60	2	A:138-187 B:138-186 (gaps) -	50 49 -
1.10	ENST00000284049	10	ENSE00001013119	chr5:98233024-98232897	128	CHD1_HUMAN	456-498	43	0	-	-
1.11	ENST00000284049	11	ENSE00001013116	chr5:98232146-98231930	217	CHD1_HUMAN	498-570	73	0	-	-
1.12	ENST00000284049	12	ENSE00001013097	chr5:98230390-98230301	90	CHD1_HUMAN	571-600	30	0	-	-
1.13	ENST00000284049	13	ENSE00001013099	chr5:98229310-98229120	191	CHD1_HUMAN	601-664	64	0	-	-
1.14	ENST00000284049	14	ENSE00001013102	chr5:98228417-98228229	189	CHD1_HUMAN	664-727	64	0	-	-
1.15	ENST00000284049	15	ENSE00001013109	chr5:98224942-98224780	163	CHD1_HUMAN	727-781	55	0	-	-
1.16a	ENST00000284049	16a	ENSE00001013120	chr5:98223944-98223792	153	CHD1_HUMAN	782-832	51	0	-	-
1.17b	ENST00000284049	17b	ENSE00001013095	chr5:98221353-98221282	72	CHD1_HUMAN	833-856	24	0	-	-
1.18b	ENST00000284049	18b	ENSE00001013089	chr5:98218941-98218792	150	CHD1_HUMAN	857-906	50	0	-	-
1.19	ENST00000284049	19	ENSE00001013108	chr5:98217827-98217679	149	CHD1_HUMAN	907-956	50	0	-	-
1.20a	ENST00000284049	20a	ENSE00001013092	chr5:98217079-98216983	97	CHD1_HUMAN	956-988	33	0	-	-
1.21	ENST00000284049	21	ENSE00001013105	chr5:98216875-98216780	96	CHD1_HUMAN	989-1020	32	0	-	-
1.22	ENST00000284049	22	ENSE00001013113	chr5:98215432-98215256	177	CHD1_HUMAN	1021-1079	59	0	-	-
1.23	ENST00000284049	23	ENSE00001013094	chr5:98212262-98212102	161	CHD1_HUMAN	1080-1133	54	0	-	-
1.24	ENST00000284049	24	ENSE00001013115	chr5:98210817-98210776	42	CHD1_HUMAN	1133-1147	15	0	-	-
1.25	ENST00000284049	25	ENSE00001013111	chr5:98209427-98209297	131	CHD1_HUMAN	1147-1191	45	0	-	-
1.26b	ENST00000284049	26b	ENSE00001013091	chr5:98208259-98208121	139	CHD1_HUMAN	1191-1237	47	0	-	-
1.26c	ENST00000284049	26c	ENSE00001013112	chr5:98207905-98207755	151	CHD1_HUMAN	1237-1287	51	0	-	-
1.27a	ENST00000284049	27a	ENSE00001013096	chr5:98206507-98206391	117	CHD1_HUMAN	1288-1326	39	0	-	-
1.28a	ENST00000284049	28a	ENSE00001013086	chr5:98205586-98205458	129	CHD1_HUMAN	1327-1369	43	0	-	-
1.30a	ENST00000284049	30a	ENSE00001013100	chr5:98204339-98204199	141	CHD1_HUMAN	1370-1416	47	0	-	-
1.31	ENST00000284049	31	ENSE00001013087	chr5:98199290-98199112	179	CHD1_HUMAN	1417-1476	60	0	-	-
1.32d	ENST00000284049	32d	ENSE00001013093	chr5:98195772-98195676	97	CHD1_HUMAN	1476-1508	33	0	-	-
1.33	ENST00000284049	33	ENSE00001013098	chr5:98194719-98194668	52	CHD1_HUMAN	1509-1526	18	0	-	-
1.34b	ENST00000284049	34b	ENSE00001013114	chr5:98194094-98193884	211	CHD1_HUMAN	1526-1596	71	0	-	-
1.35d	ENST00000284049	35d	ENSE00002036745	chr5:98192429-98191449	981	CHD1_HUMAN	1596-1710	115	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:175
 aligned with CHD1_HUMAN | O14646 from UniProtKB/Swiss-Prot  Length:1710

    Alignment length:176
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439      
           CHD1_HUMAN   270 EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRNQ 445
               SCOP domains d2b2ya2 A:12-107 ATP-dependent helicase  CHD1 (Chromo domain protein 1)                         d2b2ya1 A:108-187 ATP-dependent helicase CHD1 (Chromo domain protein 1)          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.........hhhhhhhhh.......-.....eeeeeeee...hhhhheeehhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....eeeeeee...hhhhheeehhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CHROMO_2  PDB: A:14-106 UniProt: 272-364                                                     ------------------------CHROMO_2  PDB: A:131-185 UniProt: 389-452                 PROSITE (1)
                PROSITE (2) ------------------------------------------------CHROMO_1  PDB: A:60-8----------------------------------------------------------------------CHROMO_1             ---------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6          --------------------------------------------------------------------------Exon 1.8  PDB: A:104-138           ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.7  PDB: A:29-104 (gaps) UniProt: 287-362                             ---------------------------------Exon 1.9  PDB: A:138-187 UniProt: 396-455          Transcript 1 (2)
                 2b2y A  12 EFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFE-NKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVGRIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRKK 187
                                    21        31        41        |-|       61        71        81        91       101       111       121       131       141       151       161       171       181      
                                                                 50 |                                                                                                                                       
                                                                   52

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with CHD1_HUMAN | O14646 from UniProtKB/Swiss-Prot  Length:1710

    Alignment length:176
                                   278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438      
           CHD1_HUMAN   269 EEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVERIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRN 444
               SCOP domains d2b2yb2 B:11-107 ATP-dependent helicase C HD1 (Chromo domain protein 1)                          d2b2yb1 B:108-186 ATP-dependent he      licase CHD1 (Chromo domain protein 1)   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee......hhhhhhhhhhhhh........-.....eeeeeee...hhhhheeehhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..------...eeeee...hhhhheeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: B:14-106 UniProt: 272-364                                                     ------------------------CHROMO_2  PDB: B:131-185 UniProt: 389-452                PROSITE (1)
                PROSITE (2) -------------------------------------------------CHROMO_1  PDB: B:60-8----------------------------------------------------------------------CHROMO_1             --------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6           --------------------------------------------------------------------------Exon 1.8  PDB: B:104-138           ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.7  PDB: B:29-104 (gaps) UniProt: 287-362                             ---------------------------------Exon 1.9  PDB: B:138-186 (gaps) UniProt: 396-455  Transcript 1 (2)
                 2b2y B  11 EEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEK-KEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVGRIIAHSN------YPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRK 186
                                    20        30        40        50| |     60        70        80        90       100       110       120       130       140|      150       160       170       180      
                                                                   51 |                                                                                     141    148                                      
                                                                     53

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with CHD1_HUMAN | O14646 from UniProtKB/Swiss-Prot  Length:1710

    Alignment length:86
                                   278       288       298       308       318       328       338       348      
           CHD1_HUMAN   269 EEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK 354
               SCOP domains d2b2yc_ C: ATP-dependent helicase CHD1 (Chromo domain protein 1)                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee.....hhhhhhhhhhhhh.............eeeeeeee...hhhhheeehhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: C:14-96 UniProt: 272-364                                             PROSITE (1)
                PROSITE (2) -------------------------------------------------CHROMO_1  PDB: C:60-8---------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6           ------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.7  PDB: C:29-96 UniProt: 287-362 [INCOMPLETE]                 Transcript 1 (2)
                 2b2y C  11 EEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKK  96
                                    20        30        40        50        60        70        80        90

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Chromo domain-like (82)

Family: Chromo domain (41)

Protein domain: ATP-dependent helicase CHD1 (Chromo domain protein 1) (7)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d2b2ya1	A:108-187
1b	d2b2ya2	A:12-107
1c	d2b2yb1	B:108-186
1d	d2b2yb2	B:11-107
1e	d2b2yc_	C:

(no "CATH Domain" information available for 2B2Y)

(no "Pfam Domain" information available for 2B2Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (CHD1_HUMAN | O14646)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004003	ATP-dependent DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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: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: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: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:0043923	positive regulation by host of viral transcription	Any process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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: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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(no "Ligands, Modified Residues, Ions" information available for 2b2y)

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(no "Sites" information available for 2b2y)

	Cis Peptide Bonds
		Glu C:54 - Pro C:55	[ RasMol ]

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	2b2y
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	CHD1_HUMAN \| O14646	:	2b2t 2b2u 2b2v 2b2w 2n39 4b4c 4nw2 4o42 5afw

1kna	CRYSTAL STRUCTURE OF CHROMO DOMAIN OF HP1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING DIMETHYLLYSINE 9
1kne	CRYSTAL STRUCTURE OF CHROMO DOMAIN OF HP1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 9
1pdq	CRYSTAL STRUCTURE OF POLYCOMB CHROMODOMAIN COMPLEXED WITH THE HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 27
1q3l	CRYSTAL STRUCTURE OF CHROMODOMAIN OF HP1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING MONOMETHYLLYSINE 9
2b2t	CRYSTAL STRUCTURE OF THE TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND PHOSPHOTHREONINE 3
2b2u	CRYSTAL STRUCTURE OF THE TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND DIMETHYLARGININE 2
2b2v	CRYSTAL STRUCTURE ANALYSIS OF HUMAN CHD1 CHROMODOMAINS 1 AND 2 BOUND TO HISTONE H3 RESI 1-15 MEK4
2b2w	CRYSTAL STRUCTURE OF TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 4

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 1)

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PROSITE Motifs (2, 10)

Exons (4, 10)

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SCOP Domains (1, 5)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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