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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE ARABIDOPSIS THALIANA DISEASE RESISTANCE PROTEIN RPS4
 
Authors :  S. J. Williams, K. H. Sohn, L. Wan, M. Bernoux, Y. Ma, C. Segonzac, T. Ve, P D. J. Ericsson, S. B. Saucet, X. Zhang, J. Parker, P. N. Dodds, J. D. G. Jo B. Kobe
Date :  19 Sep 13  (Deposition) - 28 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Immune System, Plant Tir Domain, Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Williams, K. H. Sohn, L. Wan, M. Bernoux, P. F. Sarris, C. Segonzac T. Ve, Y. Ma, S. B. Saucet, D. J. Ericsson, L. W. Casey, T. Lonhienne, D. J. Winzor, X. Zhang, A. Coerdt, J. E. Parker, P. N. Dodds, B. Kobe, J. D. G. Jones
Structural Basis For Assembly And Function Of A Heterodimeric Plant Immune Receptor.
Science V. 344 299 2014
PubMed-ID: 24744375  |  Reference-DOI: 10.1126/SCIENCE.1247357

(-) Compounds

Molecule 1 - DISEASE RESISTANCE PROTEIN RPS4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN, RESIDUES 11-178
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: TIR-NBS-LRR CLASS DISEASE RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4C6R)

(-) Sites  (0, 0)

(no "Site" information available for 4C6R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4C6R)

(-) Sequences/Alignments

Asymmetric 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:162
 aligned with RPS4C_ARATH | Q9XGM3 from UniProtKB/Swiss-Prot  Length:1217

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          RPS4C_ARATH    15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c6r A  15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with RPS4C_ARATH | Q9XGM3 from UniProtKB/Swiss-Prot  Length:1217

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          RPS4C_ARATH    15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c6r B  15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain C from PDB  Type:PROTEIN  Length:162
 aligned with RPS4C_ARATH | Q9XGM3 from UniProtKB/Swiss-Prot  Length:1217

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          RPS4C_ARATH    15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhh........eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c6r C  15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain D from PDB  Type:PROTEIN  Length:162
 aligned with RPS4C_ARATH | Q9XGM3 from UniProtKB/Swiss-Prot  Length:1217

    Alignment length:162
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          RPS4C_ARATH    15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c6r D  15 QHQVFINFRGADLRRRFVSHLVTALKLNNINVFIDDYEDRGQPLDVLLKRIEESKIVLAIFSGNYTESVWCVRELEKIKDCTDEGTLVAIPIFYKLEPSTVRDLKGKFGDRFRSMAKGDERKKKWKEAFNLIPNIMGIIIDKKSVESEKVNEIVKAVKTALT 176
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   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 4C6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C6R)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RPS4C_ARATH | Q9XGM3)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009870    defense response signaling pathway, resistance gene-dependent    A series of molecular signals that depends upon R-genes and is activated during defense response.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0009626    plant-type hypersensitive response    The rapid, localized death of plant cells in response to invasion by a pathogen.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

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        RPS4C_ARATH | Q9XGM3: 4c6t

(-) Related Entries Specified in the PDB File

4c6s CRYSTAL STRUCTURE OF THE TIR DOMAIN FROM THE ARABIDOPSIS THALIANA DISEASE RESISTANCE PROTEIN RRS1
4c6t CRYSTAL STRUCTURE OF THE RPS4 AND RRS1 TIR DOMAIN HETERODIMER