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- PDB-7sa1: LRR-F-Box plant ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7sa1
TitleLRR-F-Box plant ubiquitin ligase
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 1A
KeywordsSIGNALING PROTEIN / rice D3 / ASK1 / E3-Ub ligase
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 / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / auxin polar transport ...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 / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / auxin polar transport / 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 / response to light stimulus / chromosome segregation / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / protein ubiquitination / mitochondrion / nucleus / cytosol
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / S-phase kinase-associated protein 1-like ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / 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
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / SKP1-like protein 1A / F-box/LRR-repeat MAX2 homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Oryza sativa subsp. japonica (Japanese rice)
Oryza sativa tropical japonica subgroup (rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsPalayam, M. / Shabek, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2047396 United States
CitationJournal: Nat.Plants / Year: 2022
Title: A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates strigolactone signalling.
Authors: Tal, L. / Palayam, M. / Ron, M. / Young, A. / Britt, A. / Shabek, N.
History
DepositionSep 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A
D: F-box/LRR-repeat MAX2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,24710
Polymers187,4384
Non-polymers8096
Water32418
1
A: SKP1-like protein 1A
B: F-box/LRR-repeat MAX2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2306
Polymers93,7192
Non-polymers5104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-19 kcal/mol
Surface area33480 Å2
MethodPISA
2
C: SKP1-like protein 1A
D: F-box/LRR-repeat MAX2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0174
Polymers93,7192
Non-polymers2982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-23 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.929, 79.407, 150.595
Angle α, β, γ (deg.)90.000, 127.980, 90.000
Int Tables number5
Space group name H-MC121

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


Mass: 75843.016 Da / Num. of mol.: 2 / Mutation: D720K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice), (gene. exp.) Oryza sativa tropical japonica subgroup (rice)
Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1, D3
Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5VMP0
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsNon-conserved disordered loop residues 478-515 have been eliminated for crystallization purposes by ...Non-conserved disordered loop residues 478-515 have been eliminated for crystallization purposes by introducing TEV cleavage (NLYFQS), creating fragments 1 to 477 and 516 to 720 that assembled together during purification.

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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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M Ammonium acetate, 0.1M Sodium formate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Tris, 0.1M Bicine and 30% PEG 500 ...Details: 0.1M Ammonium acetate, 0.1M Sodium formate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Tris, 0.1M Bicine and 30% PEG 500 MME and PEG 20000 at pH 8.5.
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→48.9 Å / Num. obs: 34685 / % possible obs: 97.59 % / Redundancy: 3 % / Rsym value: 0.089 / Net I/σ(I): 22.7
Reflection shellResolution: 3.21→3.32 Å / Num. unique obs: 3119 / Rsym value: 0.715

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BRP

6brp


Resolution: 3.21→48.9 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1984 5.72 %
Rwork0.2078 32686 -
obs0.211 34670 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.19 Å2 / Biso mean: 45.172 Å2 / Biso min: 1.04 Å2
Refinement stepCycle: final / Resolution: 3.21→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11656 0 54 18 11728
Biso mean--55.49 11.74 -
Num. residues----1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211968
X-RAY DIFFRACTIONf_angle_d0.45416254
X-RAY DIFFRACTIONf_dihedral_angle_d10.3851624
X-RAY DIFFRACTIONf_chiral_restr0.0391878
X-RAY DIFFRACTIONf_plane_restr0.0042090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.21-3.290.33331200.26492009212986
3.29-3.380.33441340.25772267240195
3.38-3.480.36051420.24342265240796
3.48-3.60.33941380.23612306244497
3.6-3.720.27361360.2182313244998
3.72-3.870.25671420.20342360250299
3.87-4.050.2611520.19742355250799
4.05-4.260.26791400.190723932533100
4.26-4.530.22271420.173823722514100
4.53-4.880.23271460.17123962542100
4.88-5.370.21341510.177123912542100
5.37-6.140.27681420.213923952537100
6.14-7.740.25961470.222124142561100
7.74-48.90.21951520.20752450260298

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