2GF7 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   DOUBLE TUDOR DOMAIN STRUCTURE

Authors :   Y. Huang, J. Fang, M. T. Bedford, Y. Zhang, R. M. Xu

Date :   21 Mar 06 (Deposition) - 02 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Double Tudor Domain, Tudor Tandem, Trimethyl Histone H3 Lysine 4, Trimethyl Hisone Demethylase, Jmjc Domain Containing, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Huang, J. Fang, M. T. Bedford, Y. Zhang, R. M. Xu
Recognition Of Histone H3 Lysine-4 Methylation By The Double Tudor Domain Of Jmjd2A
Science V. 312 748 2006
PubMed-ID: 16601153 | Reference-DOI: 10.1126/SCIENCE.1125162
(for further references see the PDB file header)

Molecule 1 - JUMONJI DOMAIN-CONTAINING PROTEIN 2A
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DOUBLE TUDOR DOMAIN
	Gene	:	JMJD2A, JMJD2, KIAA0677
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:229 , LYS D:910 , SER D:994 , GLN D:995	BINDING SITE FOR RESIDUE SO4 D 401
2	AC2	SOFTWARE	LYS C:910 , SER C:994 , GLN C:995	BINDING SITE FOR RESIDUE SO4 C 402
3	AC3	SOFTWARE	HOH B:91 , LYS B:910 , SER B:994 , GLN B:995	BINDING SITE FOR RESIDUE SO4 B 403
4	AC4	SOFTWARE	HOH A:278 , LYS A:910 , SER A:994 , GLN A:995	BINDING SITE FOR RESIDUE SO4 A 404

(no "SS Bond" information available for 2GF7)

Asymmetric Unit

No.	Residues
1	Leu A:1010	-	Pro A:1011
2	Leu B:1010	-	Pro B:1011
3	Leu C:1010	-	Pro C:1011
4	Leu D:1010	-	Pro D:1011

(no "SAP(SNP)/Variant" information available for 2GF7)

(no "PROSITE Motif" information available for 2GF7)

Asymmetric Unit (3, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000372396	1b	ENSE00001894244	chr1:44115829-44115923	95	KDM4A_HUMAN	-	0	0	-	-
1.3a	ENST00000372396	3a	ENSE00002186574	chr1:44118808-44118984	177	KDM4A_HUMAN	1-46	46	0	-	-
1.5	ENST00000372396	5	ENSE00001143140	chr1:44121262-44121437	176	KDM4A_HUMAN	47-105	59	0	-	-
1.6	ENST00000372396	6	ENSE00000957378	chr1:44125969-44126083	115	KDM4A_HUMAN	105-143	39	0	-	-
1.7	ENST00000372396	7	ENSE00000957379	chr1:44128565-44128758	194	KDM4A_HUMAN	144-208	65	0	-	-
1.8	ENST00000372396	8	ENSE00000957380	chr1:44131367-44131416	50	KDM4A_HUMAN	208-225	18	0	-	-
1.9b	ENST00000372396	9b	ENSE00001690958	chr1:44132123-44132226	104	KDM4A_HUMAN	225-259	35	0	-	-
1.10c	ENST00000372396	10c	ENSE00000957382	chr1:44132625-44132762	138	KDM4A_HUMAN	260-305	46	0	-	-
1.11	ENST00000372396	11	ENSE00000957383	chr1:44133443-44133690	248	KDM4A_HUMAN	306-388	83	0	-	-
1.12	ENST00000372396	12	ENSE00000957384	chr1:44134771-44134970	200	KDM4A_HUMAN	388-455	68	0	-	-
1.13b	ENST00000372396	13b	ENSE00000957385	chr1:44137176-44137546	371	KDM4A_HUMAN	455-578	124	0	-	-
1.14	ENST00000372396	14	ENSE00001080538	chr1:44149355-44149475	121	KDM4A_HUMAN	579-619	41	0	-	-
1.15	ENST00000372396	15	ENSE00000957387	chr1:44154585-44154766	182	KDM4A_HUMAN	619-679	61	0	-	-
1.16b	ENST00000372396	16b	ENSE00001143055	chr1:44156516-44156720	205	KDM4A_HUMAN	680-748	69	0	-	-
1.17	ENST00000372396	17	ENSE00001143047	chr1:44157167-44157243	77	KDM4A_HUMAN	748-773	26	0	-	-
1.18b	ENST00000372396	18b	ENSE00001143039	chr1:44157927-44157982	56	KDM4A_HUMAN	774-792	19	0	-	-
1.19	ENST00000372396	19	ENSE00001143030	chr1:44159665-44159773	109	KDM4A_HUMAN	792-828	37	0	-	-
1.20	ENST00000372396	20	ENSE00001143023	chr1:44160380-44160565	186	KDM4A_HUMAN	829-890	62	0	-	-
1.21	ENST00000372396	21	ENSE00001080535	chr1:44163514-44163684	171	KDM4A_HUMAN	891-947	57	4	A:897-947 B:897-947 C:897-947 D:897-947	51 51 51 51
1.22a	ENST00000372396	22a	ENSE00001080539	chr1:44169288-44169407	120	KDM4A_HUMAN	948-987	40	4	A:948-987 B:948-987 C:948-987 D:948-987	40 40 40 40
1.23	ENST00000372396	23	ENSE00001080536	chr1:44169691-44169783	93	KDM4A_HUMAN	988-1018	31	4	A:988-1011 B:988-1011 C:988-1011 D:988-1011	24 24 24 24
1.24a	ENST00000372396	24a	ENSE00001841454	chr1:44169901-44171186	1286	KDM4A_HUMAN	1019-1064	46	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:115
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:115
                                   906       916       926       936       946       956       966       976       986       996      1006     
         KDM4A_HUMAN    897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
               SCOP domains d2gf7a2 A:897-955 Jumonji domain-containing protein 2A     d2gf7a1 A:956-1011 Jumonji domain-containing protein 2A  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.21  PDB: A:897-947 UniProt: 891-947         Exon 1.22a  PDB: A:948-987              Exon 1.23 [INCOMPLETE]   Transcript 1
                2gf7 A  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:115
                                   906       916       926       936       946       956       966       976       986       996      1006     
         KDM4A_HUMAN    897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
               SCOP domains d2gf7b2 B:897-955 Jumonji domain-containing protein 2A     d2gf7b1 B:956-1011 Jumonji domain-containing protein 2A  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.21  PDB: B:897-947 UniProt: 891-947         Exon 1.22a  PDB: B:948-987              Exon 1.23 [INCOMPLETE]   Transcript 1
                2gf7 B  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006

Chain C from PDB  Type:PROTEIN  Length:115
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:115
                                   906       916       926       936       946       956       966       976       986       996      1006     
         KDM4A_HUMAN    897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
               SCOP domains d2gf7c2 C:897-955 Jumonji domain-containing protein 2A     d2gf7c1 C:956-1011 Jumonji domain-containing protein 2A  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.21  PDB: C:897-947 UniProt: 891-947         Exon 1.22a  PDB: C:948-987              Exon 1.23 [INCOMPLETE]   Transcript 1
                2gf7 C  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:115
                                   906       916       926       936       946       956       966       976       986       996      1006     
         KDM4A_HUMAN    897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
               SCOP domains d2gf7d2 D:897-955 Jumonji domain-containing protein 2A     d2gf7d1 D:956-1011 Jumonji domain-containing protein 2A  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhh.ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.21  PDB: D:897-947 UniProt: 891-947         Exon 1.22a  PDB: D:948-987              Exon 1.23 [INCOMPLETE]   Transcript 1
                2gf7 D  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006

Legend:		→ Mismatch	(orange background)
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	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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: Tudor domain (24)

Protein domain: Jumonji domain-containing protein 2A (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d2gf7a1	A:956-1011
1b	d2gf7b1	B:956-1011
1c	d2gf7b2	B:897-955
1d	d2gf7c1	C:956-1011
1e	d2gf7c2	C:897-955
1f	d2gf7d1	D:956-1011
1g	d2gf7d2	D:897-955
1h	d2gf7a2	A:897-955

(no "CATH Domain" information available for 2GF7)

(no "Pfam Domain" information available for 2GF7)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (KDM4A_HUMAN | O75164)

molecular function
	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:0051864	histone demethylase activity (H3-K36 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
	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: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: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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0014898	cardiac muscle hypertrophy in response to stress	The physiological enlargement or overgrowth of all or part of the heart muscle due to an increase in size (not length) of individual cardiac muscle fibers, without cell division, as a result of a disturbance in organismal or cellular homeostasis.
	GO:0070544	histone H3-K36 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
	GO:0016577	histone demethylation	The modification of histones by removal of methyl groups.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0010629	negative regulation of gene expression	Any process that decreases 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:1900113	negative regulation of histone H3-K9 trimethylation	Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation.
	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: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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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:0005721	pericentric heterochromatin	Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.

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	2gf7
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(no "Related Entries Specified in the PDB File" available for 2GF7)

Description

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