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(-) Description

Title :  TIR1-ASK1 COMPLEX STRUCTURE
 
Authors :  X. Tan, L. I. A. Calderon-Villalobos, M. Sharon, C. V. Robinson, M. Estelle, N. Zheng
Date :  05 Mar 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  F-Box, Leucine Rich Repeat, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Tan, L. I. A. Calderon-Villalobos, M. Sharon, C. Zheng, C. V. Robinson, M. Estelle, N. Zheng
Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
Nature V. 446 640 2007
PubMed-ID: 17410169  |  Reference-DOI: 10.1038/NATURE05731
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SKP1-LIKE PROTEIN 1A
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneSKP1A, ASK1, SKP1, UIP1
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymSKP1-LIKE 1, UFO-BINDING PROTEIN 1
 
Molecule 2 - TRANSPORT INHIBITOR RESPONSE 1 PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneTIR1, FBL1, WEI1
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymF-BOX/LRR-REPEAT PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:74 , HIS B:78 , LYS B:113 , ARG B:114 , ARG B:344 , ARG B:401 , ARG B:403 , ARG B:436 , ARG B:484 , LYS B:485 , ARG B:509 , HOH B:727 , HOH B:845 , HOH B:860 , HOH B:1040 , HOH B:1215 , HOH B:1232 , HOH B:1240 , HOH B:1246 , HOH B:1289BINDING SITE FOR RESIDUE IHP B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P1M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P1M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P1M)

(-) Exons   (0, 0)

(no "Exon" information available for 2P1M)

(-) 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:90
 aligned with SKP1A_ARATH | Q39255 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:153
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157   
          SKP1A_ARATH     8 LKSSDGESFEVEEAVALESQTIAHMVEDDCVDNGVPLPNVTSKILAKVIEYCKRHVEAAASKAEAVEGAATSDDDLKAWDADFMKIDQATLFELILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE 160
               SCOP domains d2p         1ma1 A:8-58             automated match                                          d2p1ma2 A:101-160 automated matches                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Skp         1_POZ-2p1mA            01 A:8-58                                                 Skp1-2p1mA02 A:101-160                                       Pfam domains
         Sec.struct. author ...---------hhhhhh.....------------.....hhhhhhhhhhh------------------------------------------hhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1m A   8 LKS---------EAVALESQTIA------------PLPNVTSKILAKVIEY------------------------------------------LILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE 160
                              |      -  |     27  |      -     |  47        57|        -         -         -         -   |   107       117       127       137       147       157   
                             10        20        30           43             58                                        101                                                           

Chain B from PDB  Type:PROTEIN  Length:567
 aligned with TIR1_ARATH | Q570C0 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:567
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       
           TIR1_ARATH    10 PEEVLEHVFSFIQLDKDRNSVSLVCKSWYEIERWCRRKVFIGNCYAVSPATVIRRFPKVRSVELKGKPHFADFNLVPDGWGGYVYPWIEAMSSSYTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVYSGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAALITIARNRPNMTRFRLCIIEPKAPDYLTLEPLDIGFGAIVEHCKDLRRLSLSGLLTDKVFEYIGTYAKKMEMLSVAFAGDSDLGMHHVLSGCDSLRKLEIRDCPFGDKALLANASKLETMRSLWMSSCSVSFGACKLLGQKMPKLNVEVIDERGAPDSRPESCPVERVFIYRTVAGPRFDMPGFVWNM 576
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh.eeee......hhhhhhhhh....eeeee..hhhhhhh.........hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh....eeeee..eeeehhhhhhhhhhh....eee....eee..hhhhhhhh........eee........hhhhhhhhhhhh....eee.....hhhhhhhhhhhh....eee........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhh...eee......hhhhhhhhhh......eeeee..hhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeeeee.............hhhhhhhhhhhh....eee.....hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhh..eeeeee....hhhhh.......eeeeee............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1m B  10 PEEVLEHVFSFIQLDKDRNSVSLVCKSWYEIERWCRRKVFIGNCYAVSPATVIRRFPKVRSVELKGKPHFADFNLVPDGWGGYVYPWIEAMSSSYTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVYSGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAALITIARNRPNMTRFRLCIIEPKAPDYLTLEPLDIGFGAIVEHCKDLRRLSLSGLLTDKVFEYIGTYAKKMEMLSVAFAGDSDLGMHHVLSGCDSLRKLEIRDCPFGDKALLANASKLETMRSLWMSSCSVSFGACKLLGQKMPKLNVEVIDERGAPDSRPESCPVERVFIYRTVAGPRFDMPGFVWNM 576
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P1M)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: POZ (36)

(-) Gene Ontology  (31, 37)

Asymmetric Unit(hide GO term definitions)
Chain A   (SKP1A_ARATH | Q39255)
molecular function
    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).
biological process
    GO:0009734    auxin-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    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:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045910    negative regulation of DNA recombination    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0046686    response to cadmium ion    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 cadmium (Cd) ion stimulus.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0009524    phragmoplast    Fibrous structure (light microscope view) that arises between the daughter nuclei at telophase and within which the initial partition (cell plate), dividing the mother cell in two (cytokinesis), is formed. Appears at first as a spindle connected to the two nuclei, but later spreads laterally in the form of a ring. Consists of microtubules.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

Chain B   (TIR1_ARATH | Q570C0)
molecular function
    GO:0010011    auxin binding    Interacting selectively and non-covalently with auxin, plant hormones that regulate aspects of plant growth.
    GO:0038198    auxin receptor activity    Combining with auxin and transmitting the signal in the cell to initiate a change in cell activity. Auxin is a plant hormone (phytohormone).
    GO:0000822    inositol hexakisphosphate binding    Interacting selectively and non-covalently with inositol hexakisphosphate.
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0009734    auxin-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0016036    cellular response to phosphate starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
    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: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:0010311    lateral root formation    The process that gives rise to a lateral root. This process pertains to the initial formation of a structure from unspecified parts. A lateral root primordium represents an organized group of cells derived from the root pericycle that will differentiate into a new root, as opposed to the initiation of the main root from the embryo proper.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0010152    pollen maturation    The final stages of microgametogenesis after the trinucleate stage has been reached resulting in viable pollen grains.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0009733    response to auxin    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 an auxin stimulus.
    GO:0002237    response to molecule of bacterial origin    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0048443    stamen development    The process whose specific outcome is the progression of the stamen over time, from its formation to the mature structure.
cellular component
    GO:0019005    SCF ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1).
    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)

UniProtKB/Swiss-Prot
        SKP1A_ARATH | Q392552p1n 2p1o 2p1p 2p1q 3c6n 3c6o 3c6p 3ogk 3ogl 3ogm 5hyw 5hzg
        TIR1_ARATH | Q570C02p1n 2p1o 2p1p 2p1q 3c6n 3c6o 3c6p

(-) Related Entries Specified in the PDB File

2p1n 2p1o 2p1p 2p1q