1TMZ - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   TMZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF ALPHA TROPOMYOSIN, NMR, 15 STRUCTURES

Authors :   N. J. Greenfield, G. T. Montelione, S. E. Hitchcock-Degregori, R. S. Farid

Date :   20 Apr 98 (Deposition) - 17 Jun 98 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (15x)

Keywords :   Tropomyosin, Actin-Binding, Thin-Filament-Regulation, Muscle, Alpha-Helix Coiled-Coil Dimer, Gcn4, Chimeric- Peptide-Model, Dimeric Tw0-Chained Coiled-Coil (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. J. Greenfield, G. T. Montelione, R. S. Farid, S. E. Hitchcock-Degregori
The Structure Of The N-Terminus Of Striated Muscle Alpha-Tropomyosin In A Chimeric Peptide: Nuclear Magnetic Resonance Structure And Circular Dichroism Studies.
Biochemistry V. 37 7834 1998
PubMed-ID: 9601044 | Reference-DOI: 10.1021/BI973167M
(for further references see the PDB file header)

Molecule 1 - TMZIP
	Chains	:	A, B
	Engineered	:	YES
	Organism Common	:	BLACK RAT, BAKER'S YEAST
	Organism Scientific	:	RATTUS RATTUS, SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	10117,4932
	Other Details	:	SYNTHETIC CHIMERIC PEPTIDE OF THE N- TERMINUS OF RAT ALPHA-TROPOMYOSIN AND THE C-TERMINUS OF THE YEAST TRANSCRIPTION FACTOR GCN4
	Strain	:	,


NMR Structure (15x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1TMZ)

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

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

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

NMR Structure (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	2	A:5-27 B:5-27
2	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	2	A:5-5 B:5-5

NMR Structure (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000057641	1	ENSRNOE00000390314	chr8:71358063-71357844	220	TPM1_RAT	1-38	38	2	A:1-17 (gaps) B:1-17 (gaps)	38 38
1.3	ENSRNOT00000057641	3	ENSRNOE00000283808	chr8:71356731-71356606	126	TPM1_RAT	39-80	42	2	A:18-32 (gaps) B:18-32 (gaps)	32 32
1.5	ENSRNOT00000057641	5	ENSRNOE00000289049	chr8:71344964-71344831	134	TPM1_RAT	81-125	45	0	-	-
1.6	ENSRNOT00000057641	6	ENSRNOE00000337985	chr8:71342905-71342788	118	TPM1_RAT	125-164	40	0	-	-
1.7	ENSRNOT00000057641	7	ENSRNOE00000229797	chr8:71341716-71341646	71	TPM1_RAT	165-188	24	0	-	-
1.8	ENSRNOT00000057641	8	ENSRNOE00000176098	chr8:71341393-71341318	76	TPM1_RAT	188-213	26	0	-	-
1.10	ENSRNOT00000057641	10	ENSRNOE00000310303	chr8:71340384-71340322	63	TPM1_RAT	214-234	21	0	-	-
1.11	ENSRNOT00000057641	11	ENSRNOE00000229785	chr8:71340066-71339997	70	TPM1_RAT	235-258	24	0	-	-
1.15	ENSRNOT00000057641	15	ENSRNOE00000322655	chr8:71332155-71331307	849	TPM1_RAT	258-284	27	0	-	-

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:32
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:57
                                   234       244       254       264       274       
           GCN4_YEAST   225 SDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d1  tmz             a_ A :                                SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..--.hh-------------hhhh-hhhhh---------hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------BZIP  PDB: A:5-27 UniProt: 231-276            ----- PROSITE (1)
                PROSITE (2) ------BZIP_BASIC     ------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------- Transcript
                 1tmz A   1 MD--AIK-------------KKMQ-MLKLD---------NYHLENEVARLKKLVGER  32
                             |  | |  -         -|  | |  14        15        25       
                             2  3 5             6  9 |  14        15                 
                                                    10

Chain A from PDB  Type:PROTEIN  Length:32
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:70
                                    10        20        30        40        50        60        70
             TPM1_RAT     1 MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEK  70
               SCOP domains d1tmza_ A:                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh---------------------hhhhhhhhhh-h....----------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-17 (gaps)          Exon 1.3  PDB: A:18-32 (gaps)    Transcript 1
                 1tmz A   1 MDAIKKKMQMLKLDN---------------------YHLENEVARL-KKLVG----------------ER  32
                                    10    |    -         -      | 19     | |28 |       -        32
                                         15                    16       25 |  30               31 
                                                                          26

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:57
                                   234       244       254       264       274       
           GCN4_YEAST   225 SDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d1  tmz             b_ B :                                SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------bZIP_1-1tmzB01   - Pfam domains (1)
           Pfam domains (2) ---------------------------------------bZIP_1-1tmzB02   - Pfam domains (2)
         Sec.struct. author ..--.hh-------------hhhh-hhhhh---------hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------BZIP  PDB: B:5-27 UniProt: 231-276            ----- PROSITE (1)
                PROSITE (2) ------BZIP_BASIC     ------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------- Transcript
                 1tmz B   1 MD--AIK-------------KKMQ-MLKLD---------NYHLENEVARLKKLVGER  32
                             |  | |  -         -|  | |  14        15        25       
                             2  3 5             6  9 |  14        15                 
                                                    10

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:70
                                    10        20        30        40        50        60        70
             TPM1_RAT     1 MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEK  70
               SCOP domains d1tmzb_ B:                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------b---------------------ZIP_1-1tmz-B01  ---------------- - Pfam domains (1)
           Pfam domains (2) --------------b---------------------ZIP_1-1tmz-B02  ---------------- - Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhh---------------------hhhhhhhhhh-.....----------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-17 (gaps)          Exon 1.3  PDB: B:18-32 (gaps)    Transcript 1
                 1tmz B   1 MDAIKKKMQMLKLDN---------------------YHLENEVARL-KKLVG----------------ER  32
                                    10    |    -         -      | 19     | |28 |       -        32
                                         15                    16       25 |  30               31 
                                                                          26

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 "CATH Domain" information available for 1TMZ)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: bZIP (54)

Family: bZIP_1 (51)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (44)

1a	bZIP_1-1tmzB01	B:15-31
1b	bZIP_1-1tmzB02	B:15-31

NMR Structure(hide GO term definitions)

Chain A,B (GCN4_YEAST | P03069)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II 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 a core promoter for RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001084	transcription factor activity, TFIID-class binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	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.
	GO:0001190	transcriptional activator 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 increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	GO:0001191	transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. 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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0010691	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	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:0001080	nitrogen catabolite activation of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting 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:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain A,B (TPM1_RAT | P04692)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0051693	actin filament capping	The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
	GO:0060048	cardiac muscle contraction	Muscle contraction of cardiac muscle tissue.
	GO:0006936	muscle contraction	A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
	GO:0030049	muscle filament sliding	The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0032781	positive regulation of ATPase activity	Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0051496	positive regulation of stress fiber assembly	Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	GO:0043462	regulation of ATPase activity	Any process that modulates the rate of ATP hydrolysis by an ATPase.
	GO:0031529	ruffle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 1tmz)

	Sites
(no "Sites" information available for 1tmz)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tmz)

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
	1tmz
		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
	GCN4_YEAST \| P03069
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TPM1_RAT \| P04692
		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
	GCN4_YEAST \| P03069
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TPM1_RAT \| P04692
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1TMZ)

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 (2, 4)

Exons (2, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (43, 43)

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