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(-) Description

Title :  GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BY EXON 1B
 
Authors :  N. J. Greenfield, Y. J. Yuang, T. Palm, G. V. Swapna, D. Monleon, G. T. Montelione, S. E. Hitchcock-Degregori, Northeast Structural Genomics Consortium (Nesg)
Date :  19 Apr 01  (Deposition) - 03 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Tropomyosin, Exon 1B, Actin-Binding, Thin-Filament-Regulation, Non-Muscle, Alpha-Helix, Coiled-Coil, Dimer, Gcn4, Chimeric- Peptide-Model, Tw0-Chained, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. J. Greenfield, Y. J. Huang, T. Palm, G. V. Swapna, D. Monleon, G. T. Montelione, S. E. Hitchcock-Degregori
Solution Nmr Structure And Folding Dynamics Of The N Terminus Of A Rat Non-Muscle Alpha-Tropomyosin In An Engineered Chimeric Protein.
J. Mol. Biol. V. 312 833 2001
PubMed-ID: 11575936  |  Reference-DOI: 10.1006/JMBI.2001.4982
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX HTA
    Expression System StrainDH5
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonNORWAY RAT, BAKER'S YEAST
    Organism ScientificRATTUS NORVEGICUS, SACCHAROMYCES CEREVISIAE
    Organism Taxid10116,4932
    Other DetailsTHE CHIMERA CONSISTS OF AN INITIAL GLY, RESIDUES 2-20 OF TROPOMYOSIN ALPHA CHAIN, BRAIN-3 AND RESIDUES 21-38 OF GENERAL CONTROL PROTEIN GCN4.
    Strain,

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1IHQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

NMR Structure (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.GCN4_YEAST231-276
 
  2A:8-33
B:8-33
2BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.GCN4_YEAST231-245
 
  2A:8-15
B:8-15
3TROPOMYOSINPS00326 Tropomyosins signature.TPM1_RAT232-240
 
  2A:37-37
B:37-37

(-) Exons   (4, 8)

NMR Structure (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000576411ENSRNOE00000390314chr8:71358063-71357844220TPM1_RAT1-38380--
1.3ENSRNOT000000576413ENSRNOE00000283808chr8:71356731-71356606126TPM1_RAT39-80420--
1.5ENSRNOT000000576415ENSRNOE00000289049chr8:71344964-71344831134TPM1_RAT81-125450--
1.6ENSRNOT000000576416ENSRNOE00000337985chr8:71342905-71342788118TPM1_RAT125-164400--
1.7ENSRNOT000000576417ENSRNOE00000229797chr8:71341716-7134164671TPM1_RAT165-188242A:1-3
B:1-3
3
3
1.8ENSRNOT000000576418ENSRNOE00000176098chr8:71341393-7134131876TPM1_RAT188-213262A:3-21 (gaps)
B:3-21 (gaps)
26
26
1.10ENSRNOT0000005764110ENSRNOE00000310303chr8:71340384-7134032263TPM1_RAT214-234212A:22-37 (gaps)
B:22-37 (gaps)
21
21
1.11ENSRNOT0000005764111ENSRNOE00000229785chr8:71340066-7133999770TPM1_RAT235-258242A:38-38
B:38-38
1
1
1.15ENSRNOT0000005764115ENSRNOE00000322655chr8:71332155-71331307849TPM1_RAT258-284270--

(-) 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:38
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:89
                                   202       212       222       232       242       252       262       272         
           GCN4_YEAST   193 GKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d                            1ihq         a_ A: G lytm1b             zip                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------------------....---------hhhhhhh-hhhhhh-------------hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------BZIP  PDB: A:8-33 UniProt: 231-276            ----- PROSITE (1)
                PROSITE (2) --------------------------------------BZIP_BASIC     ------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1ihq A   1 G----------------------------AGSS---------SLEAVRR-KIRSLQ-------------EQNYHLENEVARLKKLVGER  38
                            |        -         -         2  |      -  |     |-|    |   -        19        29         
                            |                            2  5         6    12 |   18            19                   
                            1                                                13                                      

Chain A from PDB  Type:PROTEIN  Length:38
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:50
                                   195       205       215       225       235
             TPM1_RAT   186 SEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEA 235
               SCOP domains d1i     hqa_ A: Glytm1bzi  p                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ...-----..hhhhhhhhhhhhhhh--hh-----hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------TROP PROSITE (3)
           Transcript 1 (1) 1.7-------------------------Exon 1.10            1 Transcript 1 (1)
           Transcript 1 (2) --Exon 1.8 UniProt: 188-213 ---------------------- Transcript 1 (2)
                 1ihq A   1 GAG-----SSSLEAVRRKIRSLQEQ--NY-----HLENEVARLKKLVGER  38
                              |     |5        15    |  ||-    |   28        38
                              3     4              20 21|    23               
                                                       22                     

Chain B from PDB  Type:PROTEIN  Length:38
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:89
                                   202       212       222       232       242       252       262       272         
           GCN4_YEAST   193 GKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d                            1ihq         b_ B: G lytm1b             zip                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------------------....---------hhhhhhh-hhhhhh-------------hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------BZIP  PDB: B:8-33 UniProt: 231-276            ----- PROSITE (1)
                PROSITE (2) --------------------------------------BZIP_BASIC     ------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1ihq B   1 G----------------------------AGSS---------SLEAVRR-KIRSLQ-------------EQNYHLENEVARLKKLVGER  38
                            |        -         -         2  |      -  |     |-|    |   -        19        29         
                            1                            2  5         6    12 |   18            19                   
                                                                             13                                      

Chain B from PDB  Type:PROTEIN  Length:38
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:50
                                   195       205       215       225       235
             TPM1_RAT   186 SEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEA 235
               SCOP domains d1i     hqb_ B: Glytm1bzi  p                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ...-----..hhhhhhhhhhhhhhh--hh-----hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------TROP PROSITE (3)
           Transcript 1 (1) 1.7-------------------------Exon 1.10            1 Transcript 1 (1)
           Transcript 1 (2) --Exon 1.8 UniProt: 188-213 ---------------------- Transcript 1 (2)
                 1ihq B   1 GAG-----SSSLEAVRRKIRSLQEQ--NY-----HLENEVARLKKLVGER  38
                              |     |5        15    |  ||-    |   28        38
                              3     4              20 21|    23               
                                                       22                     

   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  (1, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1IHQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IHQ)

(-) Gene Ontology  (43, 43)

NMR Structure(hide GO term definitions)
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.

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GCN4_YEAST | P030691ce9 1dgc 1env 1fav 1fmh 1gcl 1gcm 1gk6 1gzl 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2ahp 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2efr 2efs 2g9j 2hy6 2ipz 2k8x 2lpb 2n9b 2nrn 2o7h 2ovn 2vky 2vnl 2wg5 2wg6 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2yny 2ynz 2yo0 2yo1 2yo2 2yo3 2z5h 2z5i 2zta 3azd 3bas 3bat 3ck4 3crp 3g9r 3gjp 3i1g 3i5c 3k7z 3m48 3p8m 3zmf 4c46 4dmd 4g2k 4hu5 4hu6 4niz 4nj0 4nj1 4nj2 4owi 4tl1 5app 5apq 5aps 5apt 5apu 5apv 5apw 5apx 5apy 5apz 5iew 5iir 5iiv 5kht
        TPM1_RAT | P046921mv4 1tmz 2b9c 2g9j 3azd

(-) Related Entries Specified in the PDB File

1tmz A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT LONG ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BY EXON 1A RELATED ID: OR1 RELATED DB: TARGETDB