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- PDB-2zsh: Structural basis of gibberellin(GA3)-induced DELLA recognition by... -

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Basic information

Entry
Database: PDB / ID: 2zsh
TitleStructural basis of gibberellin(GA3)-induced DELLA recognition by the gibberellin receptor
Components
  • DELLA protein GAI
  • Probable gibberellin receptor GID1L1
KeywordsHormone Receptor / Plant Hormone Receptor / Gibberellin / DELLA / Gibberellin signaling pathway / Hydrolase / Nucleus / Receptor / Developmental protein / Phosphoprotein / Repressor / Transcription / Transcription regulation / Ubl conjugation
Function / homology
Function and homology information


phloem transport / gibberellic acid homeostasis / fruit morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / raffinose family oligosaccharide biosynthetic process ...phloem transport / gibberellic acid homeostasis / fruit morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / raffinose family oligosaccharide biosynthetic process / floral organ morphogenesis / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway / salicylic acid mediated signaling pathway / meiotic cytokinesis / positive regulation of fertilization / response to gibberellin / gibberellic acid mediated signaling pathway / regulation of seed germination / response to ethylene / jasmonic acid mediated signaling pathway / response to far red light / hyperosmotic salinity response / Hydrolases / response to abscisic acid / regulation of nitrogen utilization / regulation of reactive oxygen species metabolic process / cellular response to hypoxia / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Transcriptional regulator DELLA, N-terminal domain / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. ...Transcriptional regulator DELLA, N-terminal domain / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GIBBERELLIN A3 / DELLA protein GAI / Gibberellin receptor GID1A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMurase, K. / Hirano, Y. / Sun, T.P. / Hakoshima, T.
CitationJournal: Nature / Year: 2008
Title: Gibberellin-induced DELLA recognition by the gibberellin receptor GID1
Authors: Murase, K. / Hirano, Y. / Sun, T.-P. / Hakoshima, T.
History
DepositionSep 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable gibberellin receptor GID1L1
B: DELLA protein GAI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9023
Polymers51,5562
Non-polymers3461
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-25 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.018, 82.018, 130.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

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Components

#1: Protein Probable gibberellin receptor GID1L1 / GID1a / GID1-like protein 1


Mass: 39276.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q9MAA7
#2: Protein DELLA protein GAI / Gibberellic acid-insensitive mutant protein / Restoration of growth on ammonia protein 2


Mass: 12279.544 Da / Num. of mol.: 1 / Fragment: DELLA domain, UNP residues 11-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAI / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q9LQT8
#3: Chemical ChemComp-GA3 / GIBBERELLIN A3 / (1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epo xymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid


Mass: 346.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22O6 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 0.8M LiCl2, 26% PEG 4000, 1mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.99533 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99533 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 42175 / Num. obs: 42175 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.129 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3959 -random
Rwork0.205 ---
all-41877 --
obs-39256 100 %-
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2--1.03 Å20 Å2
3----2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 25 216 3375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcangle_it1.95
X-RAY DIFFRACTIONc_mcbond_it1.27
LS refinement shellResolution: 1.8→1.91 Å
RfactorNum. reflection% reflection
Rfree0.259 669 -
Rwork0.223 --
obs-6056 88.2 %

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