[English] 日本語
Yorodumi
- PDB-3ogm: Structure of COI1-ASK1 in complex with coronatine and the JAZ1 degron -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ogm
TitleStructure of COI1-ASK1 in complex with coronatine and the JAZ1 degron
Components
  • Coronatine-insensitive protein 1
  • JAZ1 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 / shade avoidance / regulation of jasmonic acid mediated signaling pathway / regulation of defense response / anther dehiscence / extracellular ATP signaling / response to insect / negative regulation of defense response / regulation of flower development ...jasmonic acid and ethylene-dependent systemic resistance / regulation of cellular response to alkaline pH / shade avoidance / regulation of jasmonic acid mediated signaling pathway / regulation of defense response / anther dehiscence / extracellular ATP signaling / response to insect / negative regulation of defense response / regulation of flower development / stamen development / stomatal movement / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / flower development / response to far red light / 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 / defense response to bacterium / protein ubiquitination / 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 / Transport inhibitor response 1 protein domain / COI1, 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 / Transport inhibitor response 1 protein domain / COI1, F-box / F-box / 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: 3.34 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SKP1-like protein 1A
B: Coronatine-insensitive protein 1
Q: JAZ1 degron peptide
C: SKP1-like protein 1A
D: Coronatine-insensitive protein 1
R: JAZ1 degron peptide
E: SKP1-like protein 1A
F: Coronatine-insensitive protein 1
S: JAZ1 degron peptide
G: SKP1-like protein 1A
H: Coronatine-insensitive protein 1
I: SKP1-like protein 1A
J: Coronatine-insensitive protein 1
U: JAZ1 degron peptide
K: SKP1-like protein 1A
L: Coronatine-insensitive protein 1
V: JAZ1 degron peptide
M: SKP1-like protein 1A
N: Coronatine-insensitive protein 1
W: JAZ1 degron peptide
O: SKP1-like protein 1A
P: Coronatine-insensitive protein 1
X: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)708,81463
Polymers703,20423
Non-polymers5,61040
Water00
1
A: SKP1-like protein 1A
B: Coronatine-insensitive protein 1
Q: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-50 kcal/mol
Surface area30920 Å2
MethodPISA
2
C: SKP1-like protein 1A
D: Coronatine-insensitive protein 1
R: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-49 kcal/mol
Surface area30940 Å2
MethodPISA
3
E: SKP1-like protein 1A
F: Coronatine-insensitive protein 1
S: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-49 kcal/mol
Surface area30930 Å2
MethodPISA
4
O: SKP1-like protein 1A
P: Coronatine-insensitive protein 1
X: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-50 kcal/mol
Surface area30920 Å2
MethodPISA
5
I: SKP1-like protein 1A
J: Coronatine-insensitive protein 1
U: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-51 kcal/mol
Surface area30880 Å2
MethodPISA
6
K: SKP1-like protein 1A
L: Coronatine-insensitive protein 1
V: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-49 kcal/mol
Surface area30910 Å2
MethodPISA
7
M: SKP1-like protein 1A
N: Coronatine-insensitive protein 1
W: JAZ1 degron peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9278
Polymers88,2253
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-52 kcal/mol
Surface area30870 Å2
MethodPISA
8
G: SKP1-like protein 1A
H: Coronatine-insensitive protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3287
Polymers85,6262
Non-polymers7015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-48 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.170, 220.758, 149.540
Angle α, β, γ (deg.)90.00, 104.45, 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

-
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 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-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
#5: Chemical...
ChemComp-PO4 / PHOSPHATE ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M ammonium phosphate, 100mM BTP, 100mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 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: 3.34→50 Å / Num. all: 95997 / Num. obs: 95997 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.34→3.41 Å / % possible all: 94.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.34→49.942 Å / SU ML: 0.43 / σ(F): 0.06 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 1876 1.95 %
Rwork0.2258 --
obs0.2266 95997 85.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.08 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.8519 Å20 Å2-1.2141 Å2
2---6.8062 Å2-0 Å2
3----8.0457 Å2
Refinement stepCycle: LAST / Resolution: 3.34→49.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46533 0 344 0 46877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147860
X-RAY DIFFRACTIONf_angle_d1.27464671
X-RAY DIFFRACTIONf_dihedral_angle_d19.35718279
X-RAY DIFFRACTIONf_chiral_restr0.0847235
X-RAY DIFFRACTIONf_plane_restr0.0058307
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A767X-RAY DIFFRACTIONPOSITIONAL
12C767X-RAY DIFFRACTIONPOSITIONAL0.046
13E767X-RAY DIFFRACTIONPOSITIONAL0.045
14G767X-RAY DIFFRACTIONPOSITIONAL0.043
15I767X-RAY DIFFRACTIONPOSITIONAL0.042
16K767X-RAY DIFFRACTIONPOSITIONAL0.042
17M767X-RAY DIFFRACTIONPOSITIONAL0.044
18O767X-RAY DIFFRACTIONPOSITIONAL0.045
21B4986X-RAY DIFFRACTIONPOSITIONAL
22D4986X-RAY DIFFRACTIONPOSITIONAL0.054
23F4986X-RAY DIFFRACTIONPOSITIONAL0.055
24J4986X-RAY DIFFRACTIONPOSITIONAL0.052
25L4986X-RAY DIFFRACTIONPOSITIONAL0.051
26N4986X-RAY DIFFRACTIONPOSITIONAL0.066
27P4986X-RAY DIFFRACTIONPOSITIONAL0.054
31Q157X-RAY DIFFRACTIONPOSITIONAL
32R157X-RAY DIFFRACTIONPOSITIONAL0.044
33S157X-RAY DIFFRACTIONPOSITIONAL0.038
34U157X-RAY DIFFRACTIONPOSITIONAL0.038
35V157X-RAY DIFFRACTIONPOSITIONAL0.04
36W157X-RAY DIFFRACTIONPOSITIONAL0.046
37X157X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.430.3341160.29615833X-RAY DIFFRACTION70
3.43-3.53090.33371400.28866782X-RAY DIFFRACTION81
3.5309-3.64490.29681330.28376951X-RAY DIFFRACTION83
3.6449-3.77510.33361500.26947145X-RAY DIFFRACTION85
3.7751-3.92620.32521420.25767250X-RAY DIFFRACTION86
3.9262-4.10480.2841450.23437388X-RAY DIFFRACTION87
4.1048-4.32110.27081460.21337394X-RAY DIFFRACTION88
4.3211-4.59170.22821500.19497562X-RAY DIFFRACTION90
4.5917-4.94590.25481510.18847568X-RAY DIFFRACTION90
4.9459-5.44310.24261510.18847559X-RAY DIFFRACTION90
5.4431-6.22940.23261500.18967575X-RAY DIFFRACTION90
6.2294-7.84350.23681530.18087610X-RAY DIFFRACTION90
7.8435-49.94780.18541490.16857504X-RAY DIFFRACTION88

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more