1Q2Z - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   THE 3D SOLUTION STRUCTURE OF THE C-TERMINAL REGION OF KU86

Authors :   R. Harris, D. Esposito, A. Sankar, J. D. Maman, J. A. Hinks, L. H. Pearl, P. C. Driscoll

Date :   28 Jul 03 (Deposition) - 13 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ku, Dna Repair, Protein Structure, Nmr Spectroscopy, Dna-Pk, Ku86, Ku80, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Harris, D. Esposito, A. Sankar, J. D. Maman, J. A. Hinks, L. H. Pearl, P. C. Driscoll
The 3D Solution Structure Of The C-Terminal Region Of Ku86 (Ku86Ctr)
J. Mol. Biol. V. 335 573 2004
PubMed-ID: 14672664 | Reference-DOI: 10.1016/J.JMB.2003.10.047
(for further references see the PDB file header)

Molecule 1 - ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET-B
	Expression System Strain	:	BL21STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	KU86CTR (591-709)
	Gene	:	XRCC5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LUPUS KU AUTOANTIGEN PROTEIN P86, KU86, KU80, 86 KDA SUBUNIT OF KU ANTIGEN, THYROID- LUPUS AUTOANTIGEN, TLAA, CTC BOX BINDING FACTOR 85 KDA SUBUNIT, CTCBF, CTC85, NUCLEAR FACTOR IV, DNA-REPAIR PROTEIN XRCC5


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Q2Z)

(no "Site" information available for 1Q2Z)

(no "SS Bond" information available for 1Q2Z)

(no "Cis Peptide Bond" information available for 1Q2Z)

(no "SAP(SNP)/Variant" information available for 1Q2Z)

(no "PROSITE Motif" information available for 1Q2Z)

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000392133	1	ENSE00001606905	chr2:216972187-216972255	69	XRCC5_HUMAN	-	0	0	-	-
1.2	ENST00000392133	2	ENSE00001685529	chr2:216972376-216972421	46	XRCC5_HUMAN	-	0	0	-	-
1.3a	ENST00000392133	3a	ENSE00001722417	chr2:216973814-216974180	367	XRCC5_HUMAN	1-7	7	0	-	-
1.5a	ENST00000392133	5a	ENSE00001702382	chr2:216977739-216977852	114	XRCC5_HUMAN	8-45	38	0	-	-
1.6b	ENST00000392133	6b	ENSE00001074754	chr2:216981382-216981565	184	XRCC5_HUMAN	46-107	62	0	-	-
1.6g	ENST00000392133	6g	ENSE00001741685	chr2:216982469-216982517	49	XRCC5_HUMAN	107-123	17	0	-	-
1.7c	ENST00000392133	7c	ENSE00001791529	chr2:216983766-216983888	123	XRCC5_HUMAN	123-164	42	0	-	-
1.8	ENST00000392133	8	ENSE00001074723	chr2:216986785-216986976	192	XRCC5_HUMAN	164-228	65	0	-	-
1.9a	ENST00000392133	9a	ENSE00000785536	chr2:216990640-216990754	115	XRCC5_HUMAN	228-266	39	0	-	-
1.10a	ENST00000392133	10a	ENSE00000785538	chr2:216992259-216992397	139	XRCC5_HUMAN	267-313	47	0	-	-
1.12	ENST00000392133	12	ENSE00000785539	chr2:216995598-216995710	113	XRCC5_HUMAN	313-350	38	0	-	-
1.13	ENST00000392133	13	ENSE00000785540	chr2:216997048-216997110	63	XRCC5_HUMAN	351-371	21	0	-	-
1.14	ENST00000392133	14	ENSE00000417070	chr2:217001811-217001948	138	XRCC5_HUMAN	372-417	46	0	-	-
1.15	ENST00000392133	15	ENSE00000785542	chr2:217002812-217002902	91	XRCC5_HUMAN	418-448	31	0	-	-
1.16	ENST00000392133	16	ENSE00000785543	chr2:217005909-217006042	134	XRCC5_HUMAN	448-492	45	0	-	-
1.17	ENST00000392133	17	ENSE00001316333	chr2:217012806-217012999	194	XRCC5_HUMAN	493-557	65	0	-	-
1.18	ENST00000392133	18	ENSE00000785545	chr2:217024791-217024884	94	XRCC5_HUMAN	557-588	32	0	-	-
1.19	ENST00000392133	19	ENSE00001312814	chr2:217026702-217026771	70	XRCC5_HUMAN	589-612	24	1	A:1-23	23
1.20	ENST00000392133	20	ENSE00001299331	chr2:217054948-217055057	110	XRCC5_HUMAN	612-648	37	1	A:23-59	37
1.21	ENST00000392133	21	ENSE00001319280	chr2:217057362-217057458	97	XRCC5_HUMAN	649-681	33	1	A:60-92	33
1.22	ENST00000392133	22	ENSE00001306763	chr2:217059642-217059709	68	XRCC5_HUMAN	681-703	23	1	A:92-114	23
1.23b	ENST00000392133	23b	ENSE00001290848	chr2:217069045-217069119	75	XRCC5_HUMAN	704-728	25	1	A:115-120	6
1.24e	ENST00000392133	24e	ENSE00001702636	chr2:217069911-217071026	1116	XRCC5_HUMAN	729-732	4	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
	(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:120
 aligned with XRCC5_HUMAN | P13010 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:120
                                   599       609       619       629       639       649       659       669       679       689       699       709
          XRCC5_HUMAN   590 GSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKD 709
               SCOP domains d1q2za_ A: C-terminal domain of Ku80                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --Ku_PK_bind-1q2zA01 A:3-119                                                                                           - Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...............hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.19  PDB: A:1-23 ------------------------------------Exon 1.21  PDB: A:60-92          ----------------------1.23b  Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.20  PDB: A:23-59              --------------------------------Exon 1.22  PDB: A:92-11------ Transcript 1 (2)
                 1q2z A   1 GPVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKD 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: C-terminal domain of Ku80 (2)

Family: C-terminal domain of Ku80 (2)

Protein domain: C-terminal domain of Ku80 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1q2za_

(no "CATH Domain" information available for 1Q2Z)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ku_PK_bind] (2)

Family: Ku_PK_bind (2)

Homo sapiens (Human) (2)

Ku_PK_bind-1q2zA01

A:3-119

NMR Structure(hide GO term definitions)

Chain A (XRCC5_HUMAN | P13010)

molecular function
	GO:0051575	5'-deoxyribose-5-phosphate lyase activity	Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.
	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:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0003691	double-stranded telomeric DNA binding	Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
	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:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	GO:0044877	macromolecular complex binding	Interacting selectively and non-covalently with any macromolecular complex.
	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:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
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:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006974	cellular response to DNA damage 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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0071481	cellular response to X-ray	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 X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
	GO:0071480	cellular response to gamma radiation	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 a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0060218	hematopoietic stem cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
	GO:1904430	negative regulation of t-circle formation	Any process that stops, prevents or reduces the frequency, rate or extent of t-circle formation.
	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:0050769	positive regulation of neurogenesis	Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
	GO:0032481	positive regulation of type I interferon production	Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0048660	regulation of smooth muscle cell proliferation	Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0043564	Ku70:Ku80 complex	Heterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0070419	nonhomologous end joining complex	A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000783	nuclear telomere cap complex	A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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(no "Cis Peptide Bonds" information available for 1q2z)

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5221	RESONANCE ASSIGNMENT FOR C-TERMINAL REGION OF KU86

Description

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Ligands, Modified Residues, Ions (0, 0)

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Exons (5, 5)

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