1ITY - JenaLib

NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HUMAN TRF1

Authors :   T. Nishikawa, H. Okamura, A. Nagadoi, P. Konig, D. Rhodes, Y. Nishimura, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   15 Feb 02 (Deposition) - 06 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (25x)
NMR Structure *: A  (1x)

Keywords :   Helix-Turn-Helix, Telomeres, Dna Binding, Myb Domain, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nishikawa, H. Okamura, A. Nagadoi, P. Konig, D. Rhodes, Y. Nishimura
Solution Structure Of A Telomeric Dna Complex Of Human Trf1
Structure V. 9 1237 2001
PubMed-ID: 11738049 | Reference-DOI: 10.1016/S0969-2126(01)00688-8
(for further references see the PDB file header)

Molecule 1 - TRF1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET13A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN
	Gene	:	TRF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TELOMERIC REPEAT BINDING FACTOR 1

		1
NMR Structure (25x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1ITY)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MYB	PS51294	Myb-type HTH DNA-binding domain profile.	TERF1_HUMAN	375-432	1	A:375-432

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MYB	PS51294	Myb-type HTH DNA-binding domain profile.	TERF1_HUMAN	375-432	1	A:375-432

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000276603	1a	ENSE00001408652	chr8:73921099-73921440	342	TERF1_HUMAN	1-107	107	0	-	-
1.3	ENST00000276603	3	ENSE00000980813	chr8:73926130-73926225	96	TERF1_HUMAN	107-139	33	0	-	-
1.4	ENST00000276603	4	ENSE00000980814	chr8:73932919-73933040	122	TERF1_HUMAN	139-179	41	0	-	-
1.5b	ENST00000276603	5b	ENSE00000980815	chr8:73934451-73934537	87	TERF1_HUMAN	180-208	29	0	-	-
1.6	ENST00000276603	6	ENSE00000980816	chr8:73937057-73937206	150	TERF1_HUMAN	209-258	50	0	-	-
1.7b	ENST00000276603	7b	ENSE00000980817	chr8:73939175-73939287	113	TERF1_HUMAN	259-296	38	0	-	-
1.8b	ENST00000276603	8b	ENSE00000980818	chr8:73942571-73942630	60	TERF1_HUMAN	296-316	21	0	-	-
1.8d	ENST00000276603	8d	ENSE00000980819	chr8:73944277-73944368	92	TERF1_HUMAN	316-347	32	0	-	-
1.10	ENST00000276603	10	ENSE00001087264	chr8:73951351-73951454	104	TERF1_HUMAN	347-381	35	1	A:373-381	9
1.11a	ENST00000276603	11a	ENSE00002096154	chr8:73958196-73958706	511	TERF1_HUMAN	382-439	58	1	A:382-439	58

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:67
 aligned with TERF1_HUMAN | P54274 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:67
                                   382       392       402       412       422       432       
          TERF1_HUMAN   373 EKHRARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKLKLISSDSED 439
               SCOP domains d1itya_ A: DNA-binding domain of human telomeric protein, hTRF1     SCOP domains
               CATH domains 1ityA00 A:373-439 Homeodomain-like                                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HTH_MYB  PDB: A:375-432 UniProt: 375-432                  ------- PROSITE
               Transcript 1 Exon 1.10Exon 1.11a  PDB: A:382-439 UniProt: 382-439                Transcript 1
                 1ity A 373 EKHRARKRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKLKLISSDSED 439
                                   382       392       402       412       422       432

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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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Homeodomain-like (373)

Family: DNA-binding domain of telomeric protein (9)

Protein domain: DNA-binding domain of human telomeric protein, hTRF1 (4)

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

d1itya_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

Human (Homo sapiens) (23)

1ityA00

A:373-439

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

NMR Structure(hide GO term definitions)

Chain A (TERF1_HUMAN | P54274)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008301	DNA binding, bending	The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
	GO:0098505	G-rich strand telomeric DNA binding	Interacting selectively and non-covalently with G-rich, single-stranded, telomere-associated DNA.
	GO:0003691	double-stranded telomeric DNA binding	Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003720	telomerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
	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:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	GO:0000086	G2/M transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0045141	meiotic telomere clustering	The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
	GO:0007094	mitotic spindle assembly checkpoint	A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
	GO:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	GO:1904911	negative regulation of establishment of RNA localization to telomere	Any process that stops, prevents or reduces the frequency, rate or extent of establishment of RNA localization to telomere.
	GO:1904914	negative regulation of establishment of macromolecular complex localization to telomere	Any process that stops, prevents or reduces the frequency, rate or extent of establishment of macromolecular complex localization to telomere.
	GO:1904850	negative regulation of establishment of protein localization to telomere	Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization to telomere.
	GO:0051974	negative regulation of telomerase activity	Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
	GO:0032214	negative regulation of telomere maintenance via semi-conservative replication	Any process that stops, prevents, or reduces the frequency, rate or extent of the semi-conservative replication of telomeric DNA.
	GO:0032211	negative regulation of telomere maintenance via telomerase	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0031116	positive regulation of microtubule polymerization	Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
	GO:0045931	positive regulation of mitotic cell cycle	Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.
	GO:1904792	positive regulation of shelterin complex assembly	Any process that activates or increases the frequency, rate or extent of shelterin complex assembly.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0016233	telomere capping	A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
	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:0007004	telomere maintenance via telomerase	The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.
	GO:0031627	telomeric loop formation	The process in which linear telomeric DNA is remodeled into duplex loops, by the invasion of a 3' single-stranded overhang into the duplex region.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	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: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:0070187	shelterin complex	A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

NMR Structure
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	TERF1_HUMAN \| P54274	:	1ba5 1h6o 1iv6 1w0t 3bqo 3l82 5hkp

1ba5	1BA5 CONTAINS THE SAME PROTEIN TRUNCATED IN N- AND C- TERMINI. RELATED ID: MY_001000018.1 RELATED DB: TARGETDB

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