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Title :   SOLUTION STRUCTURE OF THE 2ND PHD DOMAIN FROM MI2B WITH C-TERMINAL LOOP REPLACED BY CORRESPONDING LOOP FROM WSTF

Authors :   A. H. Y. Kwan, D. A. Gell, A. Verger, M. Crossley, J. M. Matthews, J. P. Mackay

Date :   02 Sep 02 (Deposition) - 22 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Phd, Zinc Finger, Protein Scaffold, Dna Binding Protein/Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. H. Y. Kwan, D. A. Gell, A. Verger, M. Crossley, J. M. Matthews, J. P. Mackay
Engineering A Protein Scaffold From A Phd Finger
Structure V. 11 803 2003
PubMed-ID: 12842043 | Reference-DOI: 10.1016/S0969-2126(03)00122-9
(for further references see the PDB file header)

Molecule 1 - MI2-BETA(CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 4) AND TRANSCRIPTION FACTOR WSTF
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-6P
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-61
	Gene	:	CHD4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE C-TERMINAL LOOP (RESIDUE 37-49) WAS REPLACED BY CORRESPONDING LOOP FROM WSTF.


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:24 , CYS A:27 , CYS A:50 , CYS A:53	BINDING SITE FOR RESIDUE ZN A 62
2	AC2	SOFTWARE	CYS A:12 , CYS A:15 , ASP A:17 , HIS A:32 , CYS A:35	BINDING SITE FOR RESIDUE ZN A 63

(no "SS Bond" information available for 1MM3)

(no "Cis Peptide Bond" information available for 1MM3)

(no "SAP(SNP)/Variant" information available for 1MM3)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	CHD4_HUMAN	370-417 449-496	1	- A:9-56
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	CHD4_HUMAN	373-414 452-493	1	- A:12-53

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000357008	1	ENSE00001414099	chr12:6716551-6716466	86	CHD4_HUMAN	-	0	0	-	-
1.2	ENST00000357008	2	ENSE00001403794	chr12:6715617-6715440	178	CHD4_HUMAN	1-34	34	0	-	-
1.3	ENST00000357008	3	ENSE00000715332	chr12:6711663-6711542	122	CHD4_HUMAN	34-74	41	0	-	-
1.4	ENST00000357008	4	ENSE00000715331	chr12:6711341-6711126	216	CHD4_HUMAN	75-146	72	0	-	-
1.5	ENST00000357008	5	ENSE00001774127	chr12:6710932-6710814	119	CHD4_HUMAN	147-186	40	0	-	-
1.6	ENST00000357008	6	ENSE00000715329	chr12:6710696-6710455	242	CHD4_HUMAN	186-267	82	0	-	-
1.7	ENST00000357008	7	ENSE00000715327	chr12:6710219-6710092	128	CHD4_HUMAN	267-309	43	0	-	-
1.8	ENST00000357008	8	ENSE00000715326	chr12:6709835-6709700	136	CHD4_HUMAN	310-355	46	0	-	-
1.9	ENST00000357008	9	ENSE00000715325	chr12:6709561-6709383	179	CHD4_HUMAN	355-414	60	0	-	-
1.10	ENST00000357008	10	ENSE00000715324	chr12:6709178-6708939	240	CHD4_HUMAN	415-494	80	1	A:1-54 (gaps)	56
1.11	ENST00000357008	11	ENSE00000715321	chr12:6707591-6707388	204	CHD4_HUMAN	495-562	68	1	A:55-61	7
1.12	ENST00000357008	12	ENSE00000715320	chr12:6707265-6707060	206	CHD4_HUMAN	563-631	69	0	-	-
1.13	ENST00000357008	13	ENSE00000715319	chr12:6705303-6705172	132	CHD4_HUMAN	631-675	45	0	-	-
1.14	ENST00000357008	14	ENSE00000715318	chr12:6704596-6704500	97	CHD4_HUMAN	675-707	33	0	-	-
1.15	ENST00000357008	15	ENSE00000715316	chr12:6703816-6703625	192	CHD4_HUMAN	708-771	64	0	-	-
1.16	ENST00000357008	16	ENSE00000715313	chr12:6702782-6702582	201	CHD4_HUMAN	772-838	67	0	-	-
1.17	ENST00000357008	17	ENSE00000715311	chr12:6702394-6702257	138	CHD4_HUMAN	839-884	46	0	-	-
1.18	ENST00000357008	18	ENSE00000715310	chr12:6701983-6701862	122	CHD4_HUMAN	885-925	41	0	-	-
1.19	ENST00000357008	19	ENSE00001754995	chr12:6701732-6701559	174	CHD4_HUMAN	925-983	59	0	-	-
1.20	ENST00000357008	20	ENSE00001800433	chr12:6701223-6701082	142	CHD4_HUMAN	983-1030	48	0	-	-
1.21	ENST00000357008	21	ENSE00000715306	chr12:6700991-6700860	132	CHD4_HUMAN	1031-1074	44	0	-	-
1.22	ENST00000357008	22	ENSE00001627364	chr12:6700749-6700632	118	CHD4_HUMAN	1075-1114	40	0	-	-
1.23	ENST00000357008	23	ENSE00001711290	chr12:6697588-6697464	125	CHD4_HUMAN	1114-1155	42	0	-	-
1.24	ENST00000357008	24	ENSE00000715303	chr12:6697115-6696878	238	CHD4_HUMAN	1156-1235	80	0	-	-
1.25	ENST00000357008	25	ENSE00000715302	chr12:6696725-6696550	176	CHD4_HUMAN	1235-1293	59	0	-	-
1.26a	ENST00000357008	26a	ENSE00001350281	chr12:6692544-6692364	181	CHD4_HUMAN	1294-1354	61	0	-	-
1.26c	ENST00000357008	26c	ENSE00001293912	chr12:6692279-6692193	87	CHD4_HUMAN	1354-1383	30	0	-	-
1.27	ENST00000357008	27	ENSE00000715298	chr12:6692102-6692014	89	CHD4_HUMAN	1383-1412	30	0	-	-
1.28	ENST00000357008	28	ENSE00000715297	chr12:6691914-6691781	134	CHD4_HUMAN	1413-1457	45	0	-	-
1.29	ENST00000357008	29	ENSE00000715296	chr12:6691447-6691303	145	CHD4_HUMAN	1457-1505	49	0	-	-
1.30	ENST00000357008	30	ENSE00000715295	chr12:6690980-6690815	166	CHD4_HUMAN	1506-1561	56	0	-	-
1.31	ENST00000357008	31	ENSE00000866932	chr12:6690554-6690457	98	CHD4_HUMAN	1561-1593	33	0	-	-
1.32	ENST00000357008	32	ENSE00000866931	chr12:6690339-6690210	130	CHD4_HUMAN	1594-1637	44	0	-	-
1.33	ENST00000357008	33	ENSE00000715293	chr12:6688083-6688012	72	CHD4_HUMAN	1637-1661	25	0	-	-
1.34	ENST00000357008	34	ENSE00000715292	chr12:6687712-6687575	138	CHD4_HUMAN	1661-1707	47	0	-	-
1.35	ENST00000357008	35	ENSE00000715291	chr12:6687303-6687195	109	CHD4_HUMAN	1707-1743	37	0	-	-
1.36	ENST00000357008	36	ENSE00000715290	chr12:6687083-6686951	133	CHD4_HUMAN	1743-1787	45	0	-	-
1.37	ENST00000357008	37	ENSE00001792380	chr12:6682435-6682240	196	CHD4_HUMAN	1788-1853	66	0	-	-
1.38	ENST00000357008	38	ENSE00001183612	chr12:6680198-6680035	164	CHD4_HUMAN	1853-1907	55	0	-	-
1.39	ENST00000357008	39	ENSE00001413114	chr12:6679859-6679249	611	CHD4_HUMAN	1908-1912	5	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:61
 aligned with CHD4_HUMAN | Q14839 from UniProtKB/Swiss-Prot  Length:1912

    Alignment length:63
                                   448       458       468       478       488       498   
           CHD4_HUMAN   439 GDLEEEDDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALKGK 501
               SCOP domains d1mm  3a_ A: Mi2-beta (CHD4)                                    SCOP domains
               CATH domains 1mm3  A00 A:1-61 Zinc/RING finger domain, C3HC4 (zinc finger)   CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....--.................ee......ee.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------ZF_PHD_2  PDB: A:9-56 UniProt: 449-496          ----- PROSITE (1)
                PROSITE (2) -------------ZF_PHD_1  PDB: A:12-53 UniProt: 452-493   -------- PROSITE (2)
               Transcript 1 Exon 1.10  PDB: A:1-54 (gaps) UniProt: 415-494          1.11    Transcript 1
                 1mm3 A   1 GPLG--SDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLRPALYEVPDGEWQCPRCTCPALKGK  61
                               |  |  8        18        28        38        48        58   
                               4  5

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: FYVE/PHD zinc finger (57)

Superfamily: FYVE/PHD zinc finger (57)

Family: PHD domain (30)

Protein domain: Mi2-beta (CHD4) (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d1mm3a_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Herpes Virus-1 (49)

Homologous Superfamily: Zinc/RING finger domain, C3HC4 (zinc finger) (47)

Human (Homo sapiens) (26)

1mm3A00

A:1-61

(no "Pfam Domain" information available for 1MM3)

NMR Structure(hide GO term definitions)

Chain A (CHD4_HUMAN | Q14839)

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:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	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:0001103	RNA polymerase II repressing transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0031492	nucleosomal DNA binding	Interacting selectively and non-covalently with the DNA portion of a nucleosome.
	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).
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0043044	ATP-dependent chromatin remodeling	Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
	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:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	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:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	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:0051225	spindle assembly	The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
	GO:0072553	terminal button organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a terminal button. A terminal button is the terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016581	NuRD complex	An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	GO:0032993	protein-DNA complex	A macromolecular complex containing both protein and DNA molecules.

NMR Structure
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	CHD4_HUMAN \| Q14839	:	1mm2 2ee1 2l5u 2l75 2n5n 4o9i

1f62	1F62 CONTAINS PHD DOMAIN FROM WSTF
1fp0	1FP0 CONTAINS PHD DOMAIN FROM KAP-1
1mm2	1MM2 CONTAINS THE 2ND PHD DOMAIN FROM MI2B

Description

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