2MNZ - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   NMR STRUCTURE OF KDM5B PHD1 FINGER IN COMPLEX WITH H3K4ME0(1-10AA)

Authors :   Y. Zhang, H. R. Yang, X. Guo, N. Y. Rong, Y. J. Song, Y. W. Xu, W. X. Lan, Y. H.

Date :   16 Apr 14 (Deposition) - 06 Aug 14 (Release) - 06 Aug 14 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Kdm5B, Phd1, H3K4, Demethylase, Repression, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, H. R. Yang, X. Guo, N. Y. Rong, Y. J. Song, Y. W. Xu, W. X. Lan, X. Zhang, M. Liu, Y. H. Xu, C. Cao
The Phd1 Finger Of Kdm5B Recognizes Unmodified H3K4 During The Demethylation Of Histone H3K4Me2/3 By Kdm5B
Protein Cell 2014
PubMed-ID: 24952722 | Reference-DOI: 10.1007/S13238-014-0078-4

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B
	Chains	:	A
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-6P-1
	Expression System Vector Type	:	VECTOR
	Fragment	:	ZINC FINGER DOMAIN PHD1, RESIDUES 306-360
	Gene	:	KDM5B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA- BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1

Molecule 2 - H3K4ME0
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SYNTHETIC PEPTIDE
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

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 * (0, 0)

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

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:312 , CYS A:315 , HIS A:335 , CYS A:338	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	CYS A:327 , CYS A:330 , ASP A:331 , CYS A:353 , CYS A:356	BINDING SITE FOR RESIDUE ZN A 402

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

(no "Cis Peptide Bond" information available for 2MNZ)

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

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.	KDM5B_HUMAN	309-359 1176-1224 1484-1538	1	A:309-359 - -
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	KDM5B_HUMAN	312-356 1179-1221	1	A:312-356 -

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.	KDM5B_HUMAN	309-359 1176-1224 1484-1538	1	A:309-359 - -
2	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	KDM5B_HUMAN	312-356 1179-1221	1	A:312-356 -

(no "Exon" information available for 2MNZ)

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:55
 aligned with KDM5B_HUMAN | Q9UGL1 from UniProtKB/Swiss-Prot  Length:1544

    Alignment length:55
                                   315       325       335       345       355     
          KDM5B_HUMAN   306 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE 360
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee.......ee.................hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZF_PHD_2  PDB: A:309-359 UniProt: 309-359          - PROSITE (1)
                PROSITE (2) ------ZF_PHD_1  PDB: A:312-356 UniProt: 312-356    ---- PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                 2mnz A 306 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE 360
                                   315       325       335       345       355

Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .ee....... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2mnz B 363 ARTKQTARKS 372
                                   372

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 2MNZ)

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

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

NMR Structure(hide GO term definitions)

Chain A (KDM5B_HUMAN | Q9UGL1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0032453	histone demethylase activity (H3-K4 specific)	Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein.
	GO:0034648	histone demethylase activity (H3-dimethyl-K4 specific)	Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein.
	GO:0034647	histone demethylase activity (H3-trimethyl-K4 specific)	Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
	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:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0060444	branching involved in mammary gland duct morphogenesis	The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
	GO:0044344	cellular response to fibroblast growth factor 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 an fibroblast growth factor stimulus.
	GO:0034720	histone H3-K4 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
	GO:0034721	histone H3-K4 demethylation, trimethyl-H3-K4-specific	The modification of histone H3 by the removal of a methyl group from a trimetylated lysine at position 4 of the histone.
	GO:0070306	lens fiber cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
	GO:0060763	mammary duct terminal end bud growth	The morphogenetic growth of the large, club-shaped terminal end of a mammary gland duct during prepubertal growth and during puberty.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0033601	positive regulation of mammary gland epithelial cell proliferation	Any process that activates or increases the rate or extent of mammary gland epithelial cell proliferation.
	GO:0009791	post-embryonic development	The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
	GO:2000864	regulation of estradiol secretion	Any process that modulates the frequency, rate or extent of estradiol secretion.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0060992	response to fungicide	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 fungicide stimulus. Fungicides are chemicals used to kill fungi.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0007338	single fertilization	The union of male and female gametes to form a zygote.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0061038	uterus morphogenesis	The process in which anatomical structures of the uterus are generated and organized.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

NMR Structure
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Description

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