3GYO - JenaLib

Title :   SE-MET RTT106P

Authors :   Y. Liu, H. Huang, Y. Shi, M. Teng

Date :   04 Apr 09 (Deposition) - 08 Dec 09 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A

Keywords :   Histone Chaperone, Chaperone, Chromosomal Protein, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Transposition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Liu, H. Huang, B. O. Zhou, S. S. Wang, Y. Hu, X. Li, J. Liu, J. Zang, L. Niu, J. Wu, J. Q. Zhou, M. Teng, Y. Shi
Structural Analysis Of Rtt106P Reveals A Dna-Binding Role Required For Heterochromatin Silencing
J. Biol. Chem. V. 285 4251 2010
PubMed-ID: 20007951 | Reference-DOI: 10.1074/JBC.M109.055996

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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
	(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:225
 aligned with RT106_YEAST | P40161 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:241
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
          RT106_YEAST    64 TDEISETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKMASFLPVPEKPNLIYLFMTYTSCEDNKFSEPVVMTLNKENTLNQFKNLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFVNSTLVDTDAEKINSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSMIDQTEYAKIDDYVKRKQMK 304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeee...eeeeeeeee......eeeeeee..eeeeeeehhhhheeeeeeee......eeeeeeee...-----...eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhh..........-----------..eeeeeee..eeeeeee...eeeee.....eeee...eeeeeee.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gyo A   5 mDEISETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKmASFLPVPEKPNLIYLFmTYTSC-----SEPVVmTLNKENTLNQFKNLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFVN-----------NSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSmTDQTEYAKIDDYVKRKQmK 245
                            |       14        24        34        44        54        64 |      74        84   |    94    |  104       114       124       134       144  |      -    |  164       174       184       194       204       214       224 |     234       244 
                            |                                                           66-MSE           83-MSE8    94    |                                             147         159                                                                226-MSE           244-MSE
                            5-MSE                                                                                        99-MSE

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RT106_YEAST | P40161)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	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.
	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).
biological process
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0070869	heterochromatin assembly involved in chromatin silencing	Any process that results in the assembly of chromatin into heterochromatin and contributes to 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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0032196	transposition	Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.
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: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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3gyo)

	Cis Peptide Bonds
		Asp A:117 - Ser A:118	[ RasMol ]
		Gly A:184 - Phe A:185	[ RasMol ]
		Lys A:187 - Pro A:188	[ RasMol ]
		Ser A:24 - Pro A:25	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3gyo
		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
	RT106_YEAST \| P40161
		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

Description