Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF MYC3 N-TERMINAL JAZ-BINDING DOMAIN [44-238] IN COMPLEX WITH JAS MOTIF OF JAZ9
 
Authors :  J. Ke, F. Zhang, X. E. Zhou, J. S. Brunzelle, M. Zhou, H. E. Xu, K. Melcher,
Date :  07 Nov 14  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helix-Sheet-Helix, Alpha+Beta Structural Fold, Transcription Factor, Bind Jaz Corepressors Or Mediator Subunit Med25, Nuclear, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Zhang, J. Yao, J. Ke, L. Zhang, V. Q. Lam, X. F. Xin, X. E. Zhou, J. Chen, J. Brunzelle, P. R. Griffin, M. Zhou, H. E. Xu, K. Melcher, S. Y. He
Structural Basis Of Jaz Repression Of Myc Transcription Factors In Jasmonate Signalling.
Nature V. 525 269 2015
PubMed-ID: 26258305  |  Reference-DOI: 10.1038/NATURE14661

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR MYC3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL JAZ-BINDING DOMAIN (UNP RESIDUES 44-238)
    Gene: AT5G46760, ATR2, BHLH5, EN36, MYC3, MZA15.18
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: BASIC HELIX-LOOP-HELIX PROTEIN 5, ATBHLH5, BHLH 5, PROTEIN ALTERED TRYPTOPHAN REGULATION 2, TRANSCRIPTION FACTOR ATR2, TRANSCRIPTION FACTOR EN 36, BHLH TRANSCRIPTION FACTOR BHLH005
 
Molecule 2 - PROTEIN TIFY 7
    Chains: B
    Engineered: YES
    Fragment: JAS MOTIF (UNP RESIDUES 218-239)
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: JASMONATE ZIM DOMAIN-CONTAINING PROTEIN 9
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4RS9)

(-) Sites  (0, 0)

(no "Site" information available for 4RS9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RS9)

(-) Exons   (0, 0)

(no "Exon" information available for 4RS9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.....eeeeeeeeeee......eeeeeeeeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh..eee..hhhhhhhhhh..eeeeehhhhhhh..hhhhhhhhhh...eeeeeee..eeeeeee......hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rs9 A  45 PQFNEDTLQQRLQALIESAGENWTYAIFWQISHDFDSSTGDNTVILGWGDGYYKGENTAEQEHRKRVIRELNSLEEVTDTEWFFLVSMTQSFVNGVGLPGESFLNSRVIWLSGSGALTGSGCERAGQGQIYGLKTMVCIATQNGVVELGSSEVISQSSDLMHKVNNLFNFN 238
                                    54        64        74        84        94     ||114       124   ||  147       157       167       177       187       197       207       217       227       237 
                                                                                 100|              128|                                                                                                
                                                                                  111               142                                                                                                


Chain B from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4rs9 B 218 SVPQARKASLARFLEKRKE 236
                                   227
   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)

(no "SCOP Domain" information available for 4RS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RS9)

(-) Gene Ontology  (17, 23)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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 4rs9)
 
  Sites
(no "Sites" information available for 4rs9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rs9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  4rs9
    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
  MYC3_ARATH | Q9FIP9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TIF7_ARATH | Q8W4J8
    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
  MYC3_ARATH | Q9FIP9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TIF7_ARATH | Q8W4J8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MYC3_ARATH | Q9FIP9: 4rqw 4rru 4ywc 4yz6 5t0f 5t0q
        TIF7_ARATH | Q8W4J8: 4ywc

(-) Related Entries Specified in the PDB File

4rqw CRYSTAL STRUCTURE OF MYC3 N-TERMINAL JAZ-BINDING DOMAIN [44-238] FROM ARABIDOPSIS
4rru CRYSTAL STRUCTURE OF MYC3 N-TERMINAL JAZ-BINDING DOMAIN [5- 242] FROM ARABIDOPSIS