2L42 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   THE SOLUTION STRUCTURE OF RAP1 BRCT DOMAIN FROM SACCHAROMYCES CEREVISIAE

Authors :   W. Zhang, J. Zhang, X. Tu

Date :   29 Sep 10 (Deposition) - 26 Jan 11 (Release) - 23 Feb 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Rap1, Brct Domain, Dna Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Zhang, J. Zhang, X. Zhang, C. Xu, X. Tu
Solution Structure Of Rap1 Brct Domain From Saccharomyces Cerevisiae Reveals A Novel Fold
Biochem. Biophys. Res. Commun. V. 404 1055 2011
PubMed-ID: 21187076 | Reference-DOI: 10.1016/J.BBRC.2010.12.109

Molecule 1 - DNA-BINDING PROTEIN RAP1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET22
	Expression System Vector Type	:	VECTOR
	Fragment	:	BRCT DOMAIN, UNP RESIDUES 116-212
	Gene	:	RAP1, GRF1, TUF1, YNL216W, N1310
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN, SBF-E, TUF

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2L42)

(no "Site" information available for 2L42)

(no "SS Bond" information available for 2L42)

(no "Cis Peptide Bond" information available for 2L42)

(no "SAP(SNP)/Variant" information available for 2L42)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	RAP1_YEAST	121-208	1	A:6-93

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	RAP1_YEAST	121-208	1	A:6-93

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL216W	1	YNL216W.1	XIV:241690-244173	2484	RAP1_YEAST	1-827	827	1	A:1-97	97

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:97
 aligned with RAP1_YEAST | P11938 from UniProtKB/Swiss-Prot  Length:827

    Alignment length:97
                                   125       135       145       155       165       175       185       195       205       
           RAP1_YEAST   116 EKKEQVSGPPLSNMKFYLNRDADAHDSLNDIDQLARLIRANGGEVLDSKPRESKENVFIVSPYNHTNLPTVTPTYIKACCQSNSLLNMENYLVPYDN 212
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee...........hhhhhhhhhhh......ee.........................hhhhhhhhh...hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----BRCT  PDB: A:6-93 UniProt: 121-208                                                      ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-97 UniProt: 1-827 [INCOMPLETE]                                                 Transcript 1
                 2l42 A   1 EKKEQVSGPPLSNMKFYLNRDADAHDSLNDIDQLARLIRANGGEVLDSKPRESKENVFIVSPYNHTNLPTVTPTYIKACCQSNSLLNMENYLVPYDN  97
                                    10        20        30        40        50        60        70        80        90

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 2L42)

(no "CATH Domain" information available for 2L42)

(no "Pfam Domain" information available for 2L42)

NMR Structure(hide GO term definitions)

Chain A (RAP1_YEAST | P11938)

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:0051880	G-quadruplex DNA binding	Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome.
	GO:0001132	RNA polymerase II transcription factor activity, TBP-class protein binding	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0001094	TFIID-class transcription factor binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
	GO:0000987	core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
	GO:0031492	nucleosomal DNA binding	Interacting selectively and non-covalently with the DNA portion of a nucleosome.
	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:0000982	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
	GO:0001076	transcription factor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0071919	G-quadruplex DNA formation	A DNA metabolic process that results in the formation of G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad or G-quartet. The stacking of several layers of G-quartets forms G-quadruplexes, in which one or more DNA single strands are assembled in parallel and/or antiparallel, with interactions that can be either intra- or intermolecular in nature.
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0006348	chromatin silencing at telomere	Repression of transcription of telomeric DNA by altering the structure of chromatin.
	GO:0035390	establishment of chromatin silencing at telomere	The initial formation of a transcriptionally silent chromatin structure such as heterochromatin at the telomere.
	GO:0071169	establishment of protein localization to chromatin	The directed movement of a protein to a part of a chromosome that is organized into chromatin.
	GO:0070200	establishment of protein localization to telomere	The directed movement of a protein to a specific location in the telomeric region of a chromosome.
	GO:0031936	negative regulation of chromatin silencing	Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0031848	protection from non-homologous end joining at telomere	A process that prevents non-homologous end joining at telomere, thereby ensuring that telomeres do not fuse.
	GO:0072363	regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0010833	telomere maintenance via telomere lengthening	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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.

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2l42)

	Sites
(no "Sites" information available for 2l42)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2l42)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2l42
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RAP1_YEAST \| P11938
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RAP1_YEAST \| P11938
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RAP1_YEAST \| P11938	:	1ign 3cz6 3owt 3ukg 4bj5 4bj6 4bjt 4gfb

(no "Related Entries Specified in the PDB File" available for 2L42)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (33, 33)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File