2JX3 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DEK

Authors :   H. Matsuo, M. Devany

Date :   02 Nov 07 (Deposition) - 12 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)

Keywords :   Alpha Helix, Saf/Sap Motif, Dna Binding, Chromosomal Rearrangement, Dna-Binding, Nucleus, Phosphorylation, Proto- Oncogene, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Devany, F. Kappes, K. M. Chen, D. M. Markovitz, H. Matsuo
Solution Nmr Structure Of The N-Terminal Domain Of The Human Dek Protein
Protein Sci. V. 17 205 2008
PubMed-ID: 18227428 | Reference-DOI: 10.1110/PS.073244108
(for further references see the PDB file header)

Molecule 1 - PROTEIN DEK
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	VECTOR
	Fragment	:	SAP DOMAIN
	Gene	:	DEK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2JX3)

(no "Site" information available for 2JX3)

(no "SS Bond" information available for 2JX3)

(no "Cis Peptide Bond" information available for 2JX3)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_050949	V	140	A	DEK_HUMAN	Polymorphism	17336208	A	V	63	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2JX3)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000397239	1a	ENSE00001819650	chr6:18265054-18264616	439	DEK_HUMAN	-	0	0	-	-
1.2b	ENST00000397239	2b	ENSE00001642626	chr6:18264227-18264074	154	DEK_HUMAN	1-49	49	0	-	-
1.3b	ENST00000397239	3b	ENSE00000928752	chr6:18258636-18258535	102	DEK_HUMAN	49-83	35	1	A:1-6	6
1.4a	ENST00000397239	4a	ENSE00000848162	chr6:18258293-18258184	110	DEK_HUMAN	83-119	37	1	A:6-42	37
1.5b	ENST00000397239	5b	ENSE00000848161	chr6:18256686-18256592	95	DEK_HUMAN	120-151	32	1	A:43-74	32
1.6b	ENST00000397239	6b	ENSE00000848160	chr6:18256082-18255962	121	DEK_HUMAN	151-191	41	1	A:74-110	37
1.7a	ENST00000397239	7a	ENSE00000928751	chr6:18250070-18249882	189	DEK_HUMAN	192-254	63	0	-	-
1.9a	ENST00000397239	9a	ENSE00001007366	chr6:18237747-18237612	136	DEK_HUMAN	255-300	46	0	-	-
1.10b	ENST00000397239	10b	ENSE00000848158	chr6:18236831-18236683	149	DEK_HUMAN	300-349	50	0	-	-
1.11a	ENST00000397239	11a	ENSE00000848157	chr6:18226473-18226405	69	DEK_HUMAN	350-372	23	0	-	-
1.12d	ENST00000397239	12d	ENSE00001862786	chr6:18225961-18224099	1863	DEK_HUMAN	373-375	3	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:110
 aligned with DEK_HUMAN | P35659 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:110
                                    87        97       107       117       127       137       147       157       167       177       187
            DEK_HUMAN    78 FTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGTVSSLKKNVGQFSGFPFEKGSVQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPK 187
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------SAP-2jx3A01 A:72-106               ---- Pfam domains
         Sec.struct. author .............hhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------A----------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3b  ------------------------------------Exon 1.5b  PDB: A:43-74         ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4a  PDB: A:6-42               -------------------------------Exon 1.6b  PDB: A:74-110 [INCOMPLETE] Transcript 1 (2)
                 2jx3 A   1 FTIAQGKGQKLCEIERIHFFLSKKKTDELRNLHKLLYNRPGTVSSLKKNVGQFSGFPFEKGSVQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPK 110
                                    10        20        30        40        50        60        70        80        90       100       110

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 2JX3)

(no "CATH Domain" information available for 2JX3)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HeH (20)

Family: SAP (10)

Homo sapiens (Human) (7)

SAP-2jx3A01

A:72-106

NMR Structure(hide GO term definitions)

Chain A (DEK_HUMAN | P35659)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
biological process
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:2000779	regulation of double-strand break repair	Any process that modulates the frequency, rate or extent of double-strand break repair.
	GO:2001032	regulation of double-strand break repair via nonhomologous end joining	Any process that modulates the frequency, rate or extent of double-strand break repair via nonhomologous end joining.
	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:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
	GO:0043292	contractile fiber	Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
	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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