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(-) Description

Title :  SOLUTION STRUCTURE OF THE B3 DNA-BINDING DOMAIN OF RAV1
 
Authors :  K. Yamasaki, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna-Binding Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Tomo, N. Hayami, T. Terada, M. Shirouzu, T. Osanai, A. Tanaka, M. Seki, K. Shinozaki, S. Yokoyama
Solution Structure Of The B3 Dna Binding Domain Of The Arabidopsis Cold-Responsive Transcription Factor Rav1
Plant Cell V. 16 3448 2004
PubMed-ID: 15548737  |  Reference-DOI: 10.1105/TPC.104.026112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN RAV1
    Chains: A
    Engineered: YES
    Expression System Plasmid: PCR2.1
    Expression System Vector Type: PLASMID
    Fragment: B3 DNA-BINDING DOMAIN
    Gene: RAV1
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL-FREE SYNTHESIS
    Synonym: TRANSCRIPTION FACTOR RAV1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B3PS50863 B3 DNA-binding domain profile.RAV1_ARATH188-292  1A:188-292

(-) Exons   (0, 0)

(no "Exon" information available for 1WID)

(-) 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:117
 aligned with RAV1_ARATH | Q9ZWM9 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:117
                                   191       201       211       221       231       241       251       261       271       281       291       
           RAV1_ARATH   182 RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDLDA 298
               SCOP domains d1wida_ A: DNA-binding protein RAV1                                                                                   SCOP domains
               CATH domains 1widA00 A:182-298 At1g16640 B3 domain                                                                                 CATH domains
               Pfam domains ------B3-1widA01 A:188-292                                                                                     ------ Pfam domains
         Sec.struct. author ...eeeeeee...........eeehhhhhh..............eeeeeee...eeeeeeeeee....eeeee.hhhhhhhhh......eeeeee.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------B3  PDB: A:188-292 UniProt: 188-292                                                                      ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1wid A 182 RSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDLDA 298
                                   191       201       211       221       231       241       251       261       271       281       291
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  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, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: DNA_b-psBarrel (3)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (RAV1_ARATH | Q9ZWM9)
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:0009873    ethylene-activated signaling pathway    A series of molecular signals generated by the reception of ethylene (ethene, C2H4) by a receptor and ending with modulation of a cellular process, e.g. transcription.
    GO:0048527    lateral root development    The process whose specific outcome is the progression of the lateral root over time, from its formation to the mature structure. A lateral root is one formed from pericycle cells located on the xylem radius of the root, as opposed to the initiation of the main root from the embryo proper.
    GO:0048366    leaf development    The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.
    GO:0009910    negative regulation of flower development    Any process that stops, prevents, or reduces the frequency, rate or extent of flower development.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009741    response to brassinosteroid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a brassinosteroid stimulus.
    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.

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