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(-) Description

Title :  STRUCTURAL BASIS OF GIBBERELLIN(GA3)-INDUCED DELLA RECOGNITION BY THE GIBBERELLIN RECEPTOR
 
Authors :  K. Murase, Y. Hirano, T. P. Sun, T. Hakoshima
Date :  10 Sep 08  (Deposition) - 25 Nov 08  (Release) - 07 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plant Hormone Receptor, Gibberellin, Della, Gibberellin Signaling Pathway, Hydrolase, Nucleus, Receptor, Developmental Protein, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Murase, Y. Hirano, T. -P. Sun, T. Hakoshima
Gibberellin-Induced Della Recognition By The Gibberellin Receptor Gid1
Nature V. 456 459 2008
PubMed-ID: 19037309  |  Reference-DOI: 10.1038/NATURE07519
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE GIBBERELLIN RECEPTOR GID1L1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDFDUET-1
    Expression System StrainBL21 STAR (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymGID1A, GID1-LIKE PROTEIN 1
 
Molecule 2 - DELLA PROTEIN GAI
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET47B
    Expression System StrainBL21 STAR (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDELLA DOMAIN, UNP RESIDUES 11-113
    GeneGAI
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymGIBBERELLIC ACID-INSENSITIVE MUTANT PROTEIN, RESTORATION OF GROWTH ON AMMONIA PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GA31Ligand/IonGIBBERELLIN A3

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:27 , ARG A:35 , GLY A:115 , SER A:116 , TYR A:127 , ASP A:190 , SER A:191 , PHE A:238 , VAL A:239 , ASP A:243 , ARG A:244 , TYR A:247 , VAL A:319 , GLY A:320 , TYR A:322 , HOH A:364 , HOH A:458BINDING SITE FOR RESIDUE GA3 A 345

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:150 -Pro A:151
2Tyr A:155 -Pro A:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_GDXG_HISPS01173 Lipolytic enzymes 'G-D-X-G' family, putative histidine active site.GID1A_ARATH109-125  1A:109-125
2LIPASE_GDXG_SERPS01174 Lipolytic enzymes 'G-D-X-G' family, putative serine active site.GID1A_ARATH185-197  1A:185-197

(-) Exons   (0, 0)

(no "Exon" information available for 2ZSH)

(-) 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:338
 aligned with GID1A_ARATH | Q9MAA7 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:338
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335        
          GID1A_ARATH     6 EVNLIESRTVVPLNTWVLISNFKVAYNILRRPDGTFNRHLAEYLDRKVTANANPVDGVFSFDVLIDRRINLLSRVYRPAYADQEQPPSILDLEKPVDGDIVPVILFFHGGSFAHSSANSAIYDTLCRRLVGLCKCVVVSVNYRRAPENPYPCAYDDGWIALNWVNSRSWLKSKKDSKVHIFLAGDSSGGNIAHNVALRAGESGIDVLGNILLNPMFGGNERTESEKSLDGKYFVTVRDRDWYWKAFLPEGEDREHPACNPFSPRGKSLEGVSFPKSLVVVAGLDLIRDWQLAYAEGLKKAGQEVKLMHLEKATVGFYLLPNNNHFHNVMDEISAFVNA 343
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------Abhydrolase_3-2zshA01 A:109-323                                                                                                                                                                                        -------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhh............eeeeeeeee....eeeeeeee.......................eeeeee...........hhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhh......eeeee.........hhhhhhhh.....hhhhhhhhhhhhh...........................eeeeeee....hhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------LIPASE_GDXG_HIS  -----------------------------------------------------------LIPASE_GDXG_S-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zsh A   6 EVNLIESRTVVPLNTWVLISNFKVAYNILRRPDGTFNRHLAEYLDRKVTANANPVDGVFSFDVLIDRRINLLSRVYRPAYADQEQPPSILDLEKPVDGDIVPVILFFHGGSFAHSSANSAIYDTLCRRLVGLCKCVVVSVNYRRAPENPYPCAYDDGWIALNWVNSRSWLKSKKDSKVHIFLAGDSSGGNIAHNVALRAGESGIDVLGNILLNPMFGGNERTESEKSLDGKYFVTVRDRDWYWKAFLPEGEDREHPACNPFSPRGKSLEGVSFPKSLVVVAGLDLIRDWQLAYAEGLKKAGQEVKLMHLEKATVGFYLLPNNNHFHNVMDEISAFVNA 343
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335        

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with GAI_ARATH | Q9LQT8 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:66
                                    35        45        55        65        75        85      
            GAI_ARATH    26 GMDELLAVLGYKVRSSEMADVAQKLEQLEVMMSNVQEDDLSQLATETVHYNPAELYTWLDSMLTDL  91
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains --DELLA-2zshB01 B:28-91                                            Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhhhhhhh..-------hhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2zsh B  26 GMDELLAVLGYKVRSSEMADVAQKLEQLEVMMSNV-------LATETVHYNPAELYTWLDSMLTDL  91
                                    35        45        55    |    -  |     75        85      
                                                             60      68                       

   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 2ZSH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GID1A_ARATH | Q9MAA7)
molecular function
    GO:0010331    gibberellin binding    Interacting selectively and non-covalently with gibberellins, plant hormones that regulate aspects of plant growth.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0048444    floral organ morphogenesis    The process in which the anatomical structures of the floral organ are generated and organized.
    GO:0009740    gibberellic acid mediated signaling pathway    A series of molecular signals mediated by the detection of gibberellic acid.
    GO:0010476    gibberellin mediated signaling pathway    The series of molecular signals generated as a consequence of gibberellin stimulus.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009939    positive regulation of gibberellic acid mediated signaling pathway    Any process that activates or increases the frequency, rate or extent of gibberellic acid mediated signaling activity.
    GO:0009739    response to gibberellin    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 gibberellin stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain B   (GAI_ARATH | Q9LQT8)
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).
    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: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:0000989    transcription factor activity, transcription factor binding    Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. 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:0009740    gibberellic acid mediated signaling pathway    A series of molecular signals mediated by the detection of gibberellic acid.
    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:0009938    negative regulation of gibberellic acid mediated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of gibberellic acid mediated signaling activity.
    GO:0010233    phloem transport    The directed movement of substances, into, out of or within a cell, either in a phloem tissue or in the phloem membrane.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010218    response to far red light    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 far red light stimulus. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
    GO:0009739    response to gibberellin    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 gibberellin 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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 Related Entries

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

UniProtKB/Swiss-Prot
        GAI_ARATH | Q9LQT82zsi
        GID1A_ARATH | Q9MAA72zsi

(-) Related Entries Specified in the PDB File

2zsi