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- PDB-3ogl: Structure of COI1-ASK1 in complex with JA-isoleucine and the JAZ1... -

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Basic information

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


jasmonic acid and ethylene-dependent systemic resistance / regulation of cellular response to alkaline pH / regulation of defense response / shade avoidance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / anther dehiscence / extracellular ATP signaling / stamen development / phragmoplast ...jasmonic acid and ethylene-dependent systemic resistance / regulation of cellular response to alkaline pH / regulation of defense response / shade avoidance / negative regulation of defense response / regulation of jasmonic acid mediated signaling pathway / anther dehiscence / extracellular ATP signaling / stamen development / phragmoplast / response to insect / regulation of flower development / jasmonic acid mediated signaling pathway / response to far red light / ethylene-activated signaling pathway / stomatal movement / pollen development / response to jasmonic acid / root development / flower development / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / 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-7JA / 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: 3.18 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 17, 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

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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)708,83063
Polymers703,20423
Non-polymers5,62640
Water00
1
A: SKP1-like protein 1A
B: Coronatine-insensitive protein 1
Q: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-49 kcal/mol
Surface area30840 Å2
MethodPISA
2
C: SKP1-like protein 1A
D: Coronatine-insensitive protein 1
R: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-49 kcal/mol
Surface area30840 Å2
MethodPISA
3
E: SKP1-like protein 1A
F: Coronatine-insensitive protein 1
S: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-49 kcal/mol
Surface area30840 Å2
MethodPISA
4
G: SKP1-like protein 1A
H: Coronatine-insensitive protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3307
Polymers85,6262
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-43 kcal/mol
Surface area30950 Å2
MethodPISA
5
I: SKP1-like protein 1A
J: Coronatine-insensitive protein 1
U: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-49 kcal/mol
Surface area30770 Å2
MethodPISA
6
K: SKP1-like protein 1A
L: Coronatine-insensitive protein 1
V: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-49 kcal/mol
Surface area30820 Å2
MethodPISA
7
M: SKP1-like protein 1A
N: Coronatine-insensitive protein 1
W: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-50 kcal/mol
Surface area30660 Å2
MethodPISA
8
O: SKP1-like protein 1A
P: Coronatine-insensitive protein 1
X: JAZ1 incomplete degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9298
Polymers88,2253
Non-polymers7035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-49 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.354, 220.825, 148.674
Angle α, β, γ (deg.)90.00, 104.52, 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
112chain B or (chain A and resid 114:160)
212chain D or (chain C and resid 114:160)
312chain F or (chain E and resid 114:160)
412chain J or (chain I and resid 114:160)
512chain L or (chain K and resid 114:160)
612chain N or (chain M and resid 114:160)
712chain P 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: 2599.090 Da / Num. of mol.: 7 / Fragment: UNP RESIDUES 134-154 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q3ED96, UniProt: Q9LMA8*PLUS
#4: Chemical
ChemComp-7JA / N-({(1R,2S)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine


Type: L-peptide linking / Mass: 323.427 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H29NO4
#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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 1.7M ammonium phosphate, 100mM BTP, 100mM sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Si III channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. all: 116337 / Num. obs: 116337 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.18→3.31 Å / % possible all: 93.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.18→49.676 Å / SU ML: 0.44 / σ(F): 0.05 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 1888 1.62 %
Rwork0.215 --
obs0.2157 116337 91.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.85 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3947 Å20 Å21.6865 Å2
2--3.4766 Å20 Å2
3----6.8714 Å2
Refinement stepCycle: LAST / Resolution: 3.18→49.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46533 0 344 0 46877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01247844
X-RAY DIFFRACTIONf_angle_d1.41564607
X-RAY DIFFRACTIONf_dihedral_angle_d20.38718199
X-RAY DIFFRACTIONf_chiral_restr0.0947227
X-RAY DIFFRACTIONf_plane_restr0.0068299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A767X-RAY DIFFRACTIONPOSITIONAL
12C767X-RAY DIFFRACTIONPOSITIONAL0.056
13E767X-RAY DIFFRACTIONPOSITIONAL0.052
14G767X-RAY DIFFRACTIONPOSITIONAL0.047
15I767X-RAY DIFFRACTIONPOSITIONAL0.047
16K767X-RAY DIFFRACTIONPOSITIONAL0.047
17M767X-RAY DIFFRACTIONPOSITIONAL0.057
18O767X-RAY DIFFRACTIONPOSITIONAL0.052
21B4986X-RAY DIFFRACTIONPOSITIONAL
22D4986X-RAY DIFFRACTIONPOSITIONAL0.067
23F4986X-RAY DIFFRACTIONPOSITIONAL0.064
24J4986X-RAY DIFFRACTIONPOSITIONAL0.061
25L4986X-RAY DIFFRACTIONPOSITIONAL0.059
26N4986X-RAY DIFFRACTIONPOSITIONAL0.079
27P4986X-RAY DIFFRACTIONPOSITIONAL0.068
31Q157X-RAY DIFFRACTIONPOSITIONAL
32R157X-RAY DIFFRACTIONPOSITIONAL0.042
33S157X-RAY DIFFRACTIONPOSITIONAL0.041
34U157X-RAY DIFFRACTIONPOSITIONAL0.046
35V157X-RAY DIFFRACTIONPOSITIONAL0.043
36W157X-RAY DIFFRACTIONPOSITIONAL0.048
37X157X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.26850.38281100.31677056X-RAY DIFFRACTION73
3.2685-3.36470.41751310.30818074X-RAY DIFFRACTION83
3.3647-3.47320.33921350.28958235X-RAY DIFFRACTION86
3.4732-3.59730.32171410.25268495X-RAY DIFFRACTION88
3.5973-3.74130.28881450.23448685X-RAY DIFFRACTION90
3.7413-3.91150.2681440.21588784X-RAY DIFFRACTION91
3.9115-4.11770.23571500.20458866X-RAY DIFFRACTION92
4.1177-4.37550.23391530.18619023X-RAY DIFFRACTION93
4.3755-4.71310.22611520.1719236X-RAY DIFFRACTION96
4.7131-5.18690.21031540.1639298X-RAY DIFFRACTION97
5.1869-5.93640.22891570.17449481X-RAY DIFFRACTION98
5.9364-7.47520.24941580.18179539X-RAY DIFFRACTION98
7.4752-49.68190.20881580.18149677X-RAY DIFFRACTION99

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