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- PDB-6brq: Crystal structure of rice ASK1-D3 ubiquitin ligase complex crysta... -

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Basic information

Entry
Database: PDB / ID: 6brq
TitleCrystal structure of rice ASK1-D3 ubiquitin ligase complex crystal form 3
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 1A
KeywordsLIGASE / Ubiquitin ligase / F-box
Function / homology
Function and homology information


bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway ...bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / response to light stimulus / chromosome segregation / microtubule cytoskeleton organization / spindle / protein ubiquitination / mitochondrion / nucleus / cytosol
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SKP1-like protein 1A / F-box/LRR-repeat MAX2 homolog
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.99 Å
AuthorsShabek, N. / Zheng, N. / Mao, H. / Hinds, T.R. / Ticchiarelli, F. / Leyser, O.
CitationJournal: Nature / Year: 2018
Title: Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling.
Authors: Shabek, N. / Ticchiarelli, F. / Mao, H. / Hinds, T.R. / Leyser, O. / Zheng, N.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: F-box/LRR-repeat MAX2 homolog
A: SKP1-like protein 1A
D: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)187,4104
Polymers187,4104
Non-polymers00
Water00
1
B: F-box/LRR-repeat MAX2 homolog
A: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)93,7052
Polymers93,7052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-26 kcal/mol
Surface area29860 Å2
MethodPISA
2
D: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)93,7052
Polymers93,7052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.908, 113.306, 92.858
Angle α, β, γ (deg.)90.000, 99.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein F-box/LRR-repeat MAX2 homolog / F-box and leucine-rich repeat MAX2 homolog / Protein DWARF 3


Mass: 75828.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5VMP0
#2: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 Da / Num. of mol.: 2
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: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q39255
Sequence detailsTEV cleavage sequence (ENLYFQS) was introduced to replace the following: ...TEV cleavage sequence (ENLYFQS) was introduced to replace the following: EQPCSVANGTTTECDPEDDELGEVYESAAKKCRYMEFDD

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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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 150 mM Tris-HCL, pH 7.4, 22% MPD, 22% PEG1000, 22% P3350, 15 mM Sodium Citrate tribasic dihydrate pH 5.6, 0.45 M 1,6-Hexanediol, 5 mM DTT

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→91.71 Å / Num. obs: 31045 / % possible obs: 96.6 % / Redundancy: 3.7 % / Rsym value: 0.129 / Net I/σ(I): 26.4
Reflection shellResolution: 2.99→3.09 Å / Num. unique all: 1544 / Rsym value: 0.658

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.99→91.71 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.256 1582 RANDOM
Rwork0.22 --
Displacement parametersBiso max: 133.2 Å2 / Biso mean: 65.5451 Å2 / Biso min: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 2.99→91.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 0 0 10771
LS refinement shellResolution: 2.99→3.09 Å / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.642-0.10430.09720.0812-0.06650.48340.01420.04390.0313-0.02140.00120.0255-0.07370.0835-0.01550.0408-0.0017-0.05240.07720.00850.2728-36.114233.0042-38.2826
20.17960.2616-0.23483.95271.29631.2108-0.09550.1185-0.00110.0324-0.0448-0.03380.1434-0.31610.14020.0788-0.0441-0.05430.1725-0.010.2064-65.85216.5427-42.1818
30.50.1805-0.02730.1726-0.23820.63510.0042-0.0499-0.0541-0.0074-0.00030.01170.02940.0492-0.00380.030.0013-0.06130.07610.00430.2812.31228.3515-0.1105
41.4147-0.31880.21712.82930.12040.5268-0.1472-0.3136-0.09430.33970.1943-0.0157-0.1902-0.2219-0.04720.16220.1068-0.04250.14550.04440.0958-26.577723.24564.1711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B15 - 693
2X-RAY DIFFRACTION2A18 - 160
3X-RAY DIFFRACTION3D13 - 720
4X-RAY DIFFRACTION4C23 - 160

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