4B4C - JenaLib

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

collapse

expand

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF HUMAN CHD1.

Authors :   C. K. Allerston, C. D. O. Cooper, L. Shrestha, M. Vollmar, N. Burgess-Br W. W. Yue, E. P. Carpenter, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, O. Gileadi

Date :   30 Jul 12 (Deposition) - 15 Aug 12 (Release) - 25 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Chromodomain, Chromatin-Remodeling, Histone Acetylation Complex, Chromatin Regulation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. Allerston, C. D. O. Cooper, L. Shrestha, M. Vollmar, N. Burgess-Brown, W. W. Yue, E. P. Carpenter, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, O. Gileadi
Crystal Structure Of The Dna-Binding Domain Of Human Chd1.
To Be Published
PubMed: search

Compounds

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
	Chains	:	A
	EC Number	:	3.6.4.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING DOMAIN, RESIDUES 1119-1327
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CHD-1, CHD1, ATP-DEPENDENT HELICASE CHD1

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	6	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:1290 , ASP A:1291 , ASP A:1292 , LYS A:1295 , HOH A:2149 , HOH A:2153	BINDING SITE FOR RESIDUE SO4 A2328
2	AC2	SOFTWARE	GLU A:1146 , ARG A:1147 , ALA A:1150 , HOH A:2052	BINDING SITE FOR RESIDUE EDO A2329
3	AC3	SOFTWARE	LYS A:1139 , LEU A:1213 , HIS A:1217 , HOH A:2035	BINDING SITE FOR RESIDUE GOL A2330
4	AC4	SOFTWARE	GLY A:1271 , SER A:1272 , TRP A:1273 , GLU A:1274 , MET A:1275 , HOH A:2042 , HOH A:2185	BINDING SITE FOR RESIDUE EDO A2331
5	AC5	SOFTWARE	GLY A:1254 , LYS A:1255 , GLU A:1256 , HOH A:2121	BINDING SITE FOR RESIDUE EDO A2332
6	AC6	SOFTWARE	LYS A:1139 , HIS A:1217 , GLU A:1220 , LEU A:1221 , TYR A:1270 , HOH A:2187	BINDING SITE FOR RESIDUE EDO A2333
7	AC7	SOFTWARE	SER A:1283 , LEU A:1284 , THR A:1285 , HIS A:1286 , LYS A:1287 , HOH A:2136 , HOH A:2144	BINDING SITE FOR RESIDUE GOL A2334
8	AC8	SOFTWARE	GLN A:1301 , THR A:1304 , HOH A:2113 , HOH A:2114 , HOH A:2163	BINDING SITE FOR RESIDUE GOL A2335

SS Bonds (0, 0)

(no "SS Bond" information available for 4B4C)

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Lys A:1296	-	Pro A:1297

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 4B4C)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 4B4C)

Exons (7, 7)

Asymmetric Unit (7, 7)

	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	0	-	-
1.7	ENST00000284049	7	ENSE00001013103	chr5:98235409-98235184	226	CHD1_HUMAN	287-362	76	0	-	-
1.8	ENST00000284049	8	ENSE00001013118	chr5:98234468-98234368	101	CHD1_HUMAN	362-396	35	0	-	-
1.9	ENST00000284049	9	ENSE00001013088	chr5:98234138-98233960	179	CHD1_HUMAN	396-455	60	0	-	-
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	1	A:1124-1133	10
1.24	ENST00000284049	24	ENSE00001013115	chr5:98210817-98210776	42	CHD1_HUMAN	1133-1147	15	1	A:1133-1147	15
1.25	ENST00000284049	25	ENSE00001013111	chr5:98209427-98209297	131	CHD1_HUMAN	1147-1191	45	1	A:1147-1181	35
1.26b	ENST00000284049	26b	ENSE00001013091	chr5:98208259-98208121	139	CHD1_HUMAN	1191-1237	47	1	A:1199-1237	39
1.26c	ENST00000284049	26c	ENSE00001013112	chr5:98207905-98207755	151	CHD1_HUMAN	1237-1287	51	1	A:1237-1287	51
1.27a	ENST00000284049	27a	ENSE00001013096	chr5:98206507-98206391	117	CHD1_HUMAN	1288-1326	39	1	A:1288-1326	39
1.28a	ENST00000284049	28a	ENSE00001013086	chr5:98205586-98205458	129	CHD1_HUMAN	1327-1369	43	1	A:1327-1327	1
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	-	-

Sequences/Alignments

Asymmetric 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:187
 aligned with CHD1_HUMAN | O14646 from UniProtKB/Swiss-Prot  Length:1710

    Alignment length:204
                                  1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323    
          CHD1_HUMAN   1124 KGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALKDSSSGTERTGGRLGKVKGPTFRISGVQVNAKLVISHEEELIPLHKSIPSDPEERKQYTIPCHTKAAHFDIDWGKEDDSNLLIGIYEYGYGSWEMIKMDPDLSLTHKILPDDPDKKPQAKQLQTRADYLIKLLSRDLAKKEALSGAG 1327
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh-----------------..eeee..eeeehhhhhhhhhhhhhhhhhh..hhhhhhh................hhhhhhhhhhhhhhhh..hhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.23 -------------Exon 1.25  PDB: A:1147-1181 [INCOMPLETE]     ---------------------------------------------Exon 1.26c  PDB: A:1237-1287 UniProt: 1237-1287    Exon 1.27a  PDB: A:1288-1326           1 Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.24      -------------------------------------------Exon 1.26b  PDB: A:1199-1237 UniProt: 1191-1237------------------------------------------------------------------------------------------ Transcript 1 (2)
                4b4c A 1124 KGFSDAEIRRFIKSYKKFGGPLERLDAIARDAELVDKSETDLRRLGELVHNGCIKALK-----------------GPTFRISGVQVNAKLVISHEEELIPLHKSIPSDPEERKQYTIPCHTKAAHFDIDWGKEDDSNLLIGIYEYGYGSWEMIKMDPDLSLTHKILPDDPDKKPQAKQLQTRADYLIKLLSRDLAKKEALSGAG 1327
                                  1133      1143      1153      1163      1173       | -         -     |1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323    
                                                                                  1181              1199

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 4B4C)

CATH Domains (0, 0)

(no "CATH Domain" information available for 4B4C)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 4B4C)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

Visualization

Interactive Views

Asymmetric 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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]

	Cis Peptide Bonds
		Lys A:1296 - Pro A:1297	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4b4c
		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
	CHD1_HUMAN \| O14646
		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)
	3.6.4.12
		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

Analysis Tools

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
	CHD1_HUMAN \| O14646
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CHD1_HUMAN \| O14646	:	2b2t 2b2u 2b2v 2b2w 2b2y 2n39 4nw2 4o42 5afw

Related Entries Specified in the PDB File

2b2t	TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND PHOSPHOTHREONINE 3
2b2u	TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND DIMETHYLARGININE 2
2b2v	CRYSTAL STRUCTURE ANALYSIS OF HUMAN CHD1 CHROMODOMAINS 1AND 2 BOUND TO HISTONE H3 RESI 1-15 MEK4
2b2w	TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL CONTAINING TRIMETHYLLYSINE 4
2b2y	TANDEM CHROMODOMAINS OF HUMAN CHD1