2YUF - JenaLib

Title :   SOLUTION STRUCTURE OF THE NCD2 DOMAIN IN HUMAN TRANSCRIPTIONAL REPRESSOR NAB1 PROTEIN

Authors :   K. Saito, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   06 Apr 07 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Transcriptional Repressor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Saito, T. Kigawa, S. Yokoyama
Solution Structure Of The Ncd2 Domain In Human Transcriptional Repressor Nab1 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

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 (0, 0)

Exons (0, 0)

Sequences/Alignments

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:142
 aligned with NAB1_HUMAN | Q13506 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:219
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388         
           NAB1_HUMAN   179 GSPASPKESSEALDAAAALSVAECVERMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHKEEEIRKYSAIYGRFDSKRKDGKHLTLHELTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVEDGFPDFQDSVQTLFQQARAKSEELAALSSQQPEKVMAKQMEFLCNQAGYERLQHAERRLSAG 397
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------NCD2-2yufA01 A:8-136                                                                                                             -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....---.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---------..-----------------------------------------------------------------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yuf A   1 GSSGS---SGEALDAAAALSVAECVERMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHKEEEIRKYSAIYGRFDSKRKDGKHLTLHELTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTS---------GP-----------------------------------------------------------------SSG 142
                                |   |7        17        27        37        47        57        67        77        87        97       107       117       127       137       138|        -         -         -         -         -         -      |  
                                5   6                                                                                                                                137       138|                                                               140  
                                                                                                                                                                                139

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 (1, 1)

Gene Ontology (11, 11)

NMR Structure(hide GO term definitions)

Chain A (NAB1_HUMAN | Q13506)

molecular function
	GO:0000989	transcription factor activity, transcription factor binding	Interacting selectively and non-covalently with a specific 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.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0014037	Schwann cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of a Schwann cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.
	GO:0001958	endochondral ossification	Replacement ossification wherein bone tissue replaces cartilage.
	GO:0042552	myelination	The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
	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:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0045682	regulation of epidermis development	Any process that modulates the frequency, rate or extent of epidermis development.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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

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 2yuf)

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

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2yuf
		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
	NAB1_HUMAN \| Q13506
		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