2LLK - JenaLib

Title :   SOLUTION NMR STRUCTURE OF THE N-TERMINAL MYB-LIKE 1 DOMAIN OF THE HUMAN CYCLIN-D-BINDING TRANSCRIPTION FACTOR 1 (HDMP1), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET ID HR8011A

Authors :   M. Montecchio, A. Lemak, A. Yee, C. Xu, M. Garcia, S. Houliston, J. Min, M. Bellanda, G. T. Montelione, C. Arrowsmith, Northeast Structural Consortium (Nesg), Structural Genomics Consortium (Sgc)

Date :   10 Nov 11 (Deposition) - 23 Nov 11 (Release) - 23 Nov 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Helix Bundle, Sgc, Structural Genomics Consortium, Nesg, Northeast Structural Genomics Consortium, Cell Cycle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Montecchio, A. Lemak, A. Yee, C. Xu, M. Garcia, S. Houliston, J. Min, M. Bellanda, G. T. Montelione, C. Arrowsmith
Solution Nmr Structure Of The N-Terminal Myb-Like 1 Domain Of The Human Cyclin D Binding Transcription Factor 1 (Hdmp1).
To Be Published
PubMed: search

Compounds

Molecule 1 - CYCLIN-D-BINDING MYB-LIKE TRANSCRIPTION FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28-MHL
	Fragment	:	MYB-LIKE 1 DOMAIN RESIDUES 220-274
	Gene	:	DMTF1, DMP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HDMTF1, CYCLIN-D-INTERACTING MYB-LIKE PROTEIN 1, HDMP1

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 (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MYB_LIKE	PS50090	Myb-like domain profile.	DMTF1_HUMAN	225-263 268-329 339-388	2	A:225-263 A:268-274 -
2	HTH_MYB	PS51294	Myb-type HTH DNA-binding domain profile.	DMTF1_HUMAN	268-333	1	A:268-274

NMR Structure * (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MYB_LIKE	PS50090	Myb-like domain profile.	DMTF1_HUMAN	225-263 268-329 339-388	2	A:225-263 A:268-274 -
2	HTH_MYB	PS51294	Myb-type HTH DNA-binding domain profile.	DMTF1_HUMAN	268-333	1	A:268-274

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:55
 aligned with DMTF1_HUMAN | Q9Y222 from UniProtKB/Swiss-Prot  Length:760

    Alignment length:55
                                   229       239       249       259       269     
          DMTF1_HUMAN   220 DRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMKDTCNTG 274
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----MYB_LIKE  PDB: A:225-263               ----MYB_LIK PROSITE (1)
                PROSITE (2) ------------------------------------------------HTH_MYB PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                 2llk A 220 DRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMKDTCNTG 274
                                   229       239       249       259       269

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 (8, 8)

NMR Structure(hide GO term definitions)

Chain A (DMTF1_HUMAN | Q9Y222)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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 2llk)

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

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

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2llk
		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
	DMTF1_HUMAN \| Q9Y222
		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

Analysis Tools

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
	DMTF1_HUMAN \| Q9Y222
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description