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- PDB-3ogk: Structure of COI1-ASK1 in complex with coronatine and an incomple... -

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Basic information

Entry
Database: PDB / ID: 3ogk
TitleStructure of COI1-ASK1 in complex with coronatine and an incomplete JAZ1 degron
Components
  • Coronatine-insensitive protein 1
  • JAZ1 incomplete degron peptide
  • SKP1-like protein 1A
KeywordsPROTEIN BINDING / Leucine rich repeat / ubiquitin ligase / SCF
Function / homology
Function and homology information


jasmonic acid and ethylene-dependent systemic resistance / regulation of cellular response to alkaline pH / shade avoidance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / regulation of defense response / anther dehiscence / extracellular ATP signaling / response to insect / regulation of flower development ...jasmonic acid and ethylene-dependent systemic resistance / regulation of cellular response to alkaline pH / shade avoidance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / regulation of defense response / anther dehiscence / extracellular ATP signaling / response to insect / regulation of flower development / phragmoplast / jasmonic acid mediated signaling pathway / stamen development / ethylene-activated signaling pathway / stomatal movement / response to far red light / flower development / root development / pollen development / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / defense response to fungus / chromosome segregation / defense response / response to wounding / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / protein ubiquitination / defense response to bacterium / mitochondrion / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY / Transport inhibitor response 1 domain / COI1, F-box / F-box ...Tify domain / CO/COL/TOC1, conserved site / TIFY/JAZ family / tify domain / Jas motif / Tify domain profile. / TIFY / Transport inhibitor response 1 domain / COI1, F-box / F-box / Transport inhibitor response 1 protein domain / Monooxygenase - #50 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Monooxygenase / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Alpha-Beta Horseshoe / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-OGK / PHOSPHATE ION / Coronatine-insensitive protein 1 / SKP1-like protein 1A / Protein TIFY / Protein TIFY 10A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSheard, L.B. / Tan, X. / Mao, H. / Withers, J. / Ben-Nissan, G. / Hinds, T.R. / Hsu, F. / Sharon, M. / Browse, J. / He, S.Y. ...Sheard, L.B. / Tan, X. / Mao, H. / Withers, J. / Ben-Nissan, G. / Hinds, T.R. / Hsu, F. / Sharon, M. / Browse, J. / He, S.Y. / Rizo, J. / Howe, G.A. / Zheng, N.
CitationJournal: Nature / Year: 2010
Title: Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor.
Authors: Sheard, L.B. / Tan, X. / Mao, H. / Withers, J. / Ben-Nissan, G. / Hinds, T.R. / Kobayashi, Y. / Hsu, F.F. / Sharon, M. / Browse, J. / He, S.Y. / Rizo, J. / Howe, G.A. / Zheng, N.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SKP1-like protein 1A
B: Coronatine-insensitive protein 1
Q: JAZ1 incomplete degron peptide
C: SKP1-like protein 1A
D: Coronatine-insensitive protein 1
R: JAZ1 incomplete degron peptide
E: SKP1-like protein 1A
F: Coronatine-insensitive protein 1
S: JAZ1 incomplete degron peptide
G: SKP1-like protein 1A
H: Coronatine-insensitive protein 1
I: SKP1-like protein 1A
J: Coronatine-insensitive protein 1
U: JAZ1 incomplete degron peptide
K: SKP1-like protein 1A
L: Coronatine-insensitive protein 1
V: JAZ1 incomplete degron peptide
M: SKP1-like protein 1A
N: Coronatine-insensitive protein 1
W: JAZ1 incomplete degron peptide
O: SKP1-like protein 1A
P: Coronatine-insensitive protein 1
X: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,69063
Polymers704,08023
Non-polymers5,61040
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.847, 221.455, 148.474
Angle α, β, γ (deg.)90.00, 104.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
13
23
33
43
53
63
73

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 5:113
211chain C and resid 5:113
311chain E and resid 5:113
411chain G and resid 5:113
511chain I and resid 5:113
611chain K and resid 5:113
711chain M and resid 5:113
811chain O and resid 5:113
112(chain B and resid 12:592) or (chain A and resid 114:160)
212(chain D and resid 12:592) or (chain C and resid 114:160)
312(chain F and resid 12:592) or (chain E and resid 114:160)
412(chain J and resid 12:592) or (chain I and resid 114:160)
512(chain L and resid 12:592) or (chain K and resid 114:160)
612(chain N and resid 12:592) or (chain M and resid 114:160)
712(chain P and resid 12:592) or (chain O and resid 114:160)
113chain Q
213chain R
313chain S
413chain U
513chain V
613chain W
713chain X

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39255
#2: Protein
Coronatine-insensitive protein 1 / F-box/LRR-repeat protein 2 / AtFBL2 / AtCOI1 / COI-1


Mass: 67750.234 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COI1, FBL2, At2g39940, T28M21.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O04197
#3: Protein/peptide
JAZ1 incomplete degron peptide


Mass: 2724.196 Da / Num. of mol.: 7 / Fragment: UNP RESIDUES 139-160 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q3ED96, UniProt: Q9LMA8*PLUS
#4: Chemical
ChemComp-OGK / (1S,2S)-2-ethyl-1-({[(3aS,4S,6R,7aS)-6-ethyl-1-oxooctahydro-1H-inden-4-yl]carbonyl}amino)cyclopropanecarboxylic acid / Coronatine


Mass: 321.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H27NO4 / Comment: toxin*YM
#5: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: PO4

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M ammonium phosphate, 100mM BTP, 100mM sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2008
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 174966 / Num. obs: 174966 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→49.629 Å / SU ML: 0.45 / σ(F): 0.09 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 8777 5.02 %
Rwork0.2245 --
obs0.2267 174966 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.388 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0659 Å20 Å2-1.6663 Å2
2--3.5298 Å20 Å2
3----2.464 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46182 0 344 0 46526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447307
X-RAY DIFFRACTIONf_angle_d1.5763904
X-RAY DIFFRACTIONf_dihedral_angle_d20.35618037
X-RAY DIFFRACTIONf_chiral_restr0.1137156
X-RAY DIFFRACTIONf_plane_restr0.0068188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A759X-RAY DIFFRACTIONPOSITIONAL
12C759X-RAY DIFFRACTIONPOSITIONAL0.06
13E759X-RAY DIFFRACTIONPOSITIONAL0.06
14G759X-RAY DIFFRACTIONPOSITIONAL0.054
15I759X-RAY DIFFRACTIONPOSITIONAL0.055
16K759X-RAY DIFFRACTIONPOSITIONAL0.048
17M759X-RAY DIFFRACTIONPOSITIONAL0.055
18O759X-RAY DIFFRACTIONPOSITIONAL0.057
21B4914X-RAY DIFFRACTIONPOSITIONAL
22D4914X-RAY DIFFRACTIONPOSITIONAL0.082
23F4914X-RAY DIFFRACTIONPOSITIONAL0.074
24J4914X-RAY DIFFRACTIONPOSITIONAL0.075
25L4914X-RAY DIFFRACTIONPOSITIONAL0.07
26N4914X-RAY DIFFRACTIONPOSITIONAL0.091
27P4914X-RAY DIFFRACTIONPOSITIONAL0.078
31Q120X-RAY DIFFRACTIONPOSITIONAL
32R120X-RAY DIFFRACTIONPOSITIONAL0.038
33S120X-RAY DIFFRACTIONPOSITIONAL0.039
34U120X-RAY DIFFRACTIONPOSITIONAL0.038
35V120X-RAY DIFFRACTIONPOSITIONAL0.034
36W120X-RAY DIFFRACTIONPOSITIONAL0.038
37X120X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83150.39832190.32724357X-RAY DIFFRACTION73
2.8315-2.86480.37432400.33394798X-RAY DIFFRACTION81
2.8648-2.89970.36732520.31684925X-RAY DIFFRACTION83
2.8997-2.93640.38332830.29765002X-RAY DIFFRACTION85
2.9364-2.9750.37232670.29555173X-RAY DIFFRACTION87
2.975-3.01580.31572650.29965127X-RAY DIFFRACTION88
3.0158-3.05890.34852840.2955227X-RAY DIFFRACTION89
3.0589-3.10450.36442690.29565307X-RAY DIFFRACTION89
3.1045-3.1530.33392790.2945374X-RAY DIFFRACTION91
3.153-3.20470.35253090.27685382X-RAY DIFFRACTION92
3.2047-3.260.32332980.27015487X-RAY DIFFRACTION93
3.26-3.31920.34552760.26935543X-RAY DIFFRACTION94
3.3192-3.38310.29123130.27575593X-RAY DIFFRACTION95
3.3831-3.45210.32132940.26525626X-RAY DIFFRACTION95
3.4521-3.52710.32013120.24225653X-RAY DIFFRACTION96
3.5271-3.60920.26463070.23925693X-RAY DIFFRACTION97
3.6092-3.69940.26632800.22455813X-RAY DIFFRACTION97
3.6994-3.79940.26172960.2115729X-RAY DIFFRACTION97
3.7994-3.91110.24873000.21395764X-RAY DIFFRACTION98
3.9111-4.03730.23612850.20445791X-RAY DIFFRACTION98
4.0373-4.18160.24552940.20165828X-RAY DIFFRACTION98
4.1816-4.34890.22443070.18875875X-RAY DIFFRACTION99
4.3489-4.54670.21583250.18195792X-RAY DIFFRACTION99
4.5467-4.78620.23012930.17835908X-RAY DIFFRACTION99
4.7862-5.08580.20743240.16625862X-RAY DIFFRACTION99
5.0858-5.4780.24493420.17565832X-RAY DIFFRACTION99
5.478-6.02840.21593160.1755881X-RAY DIFFRACTION99
6.0284-6.89880.22753200.17965904X-RAY DIFFRACTION99
6.8988-8.68420.19613110.15555968X-RAY DIFFRACTION100
8.6842-49.63680.19043170.185975X-RAY DIFFRACTION99

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