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- PDB-5hyw: The crystal structure of the D3-ASK1 complex -

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Basic information

Entry
Database: PDB / ID: 5hyw
TitleThe crystal structure of the D3-ASK1 complex
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 1A
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / F-box protein / SIGNALING PROTEIN-PROTEIN BINDING complex
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 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 / S-phase kinase-associated protein 1-like ...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 / 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
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 / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsYao, R.F. / Ming, Z.H. / Yan, L.M. / Rao, Z.H. / Lou, Z.Y. / Xie, D.X.
Funding support China, 4items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31230008 China
the National Natural Science Foundation of China81322023 China
Ministry of Science and Technology2011CB915404 China
Ministry of Science and Technology2013CB911100 China
CitationJournal: Nature / Year: 2016
Title: DWARF14 is a non-canonical hormone receptor for strigolactone
Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. ...Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. / He, W. / Deng, H. / Nan, F. / Li, J. / Rao, Z. / Lou, Z. / Xie, D.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)200,3164
Polymers200,3164
Non-polymers00
Water00
1
A: F-box/LRR-repeat MAX2 homolog
B: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)100,1582
Polymers100,1582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-24 kcal/mol
Surface area28870 Å2
MethodPISA
2
C: F-box/LRR-repeat MAX2 homolog
D: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)100,1582
Polymers100,1582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.268, 79.268, 327.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 81153.680 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: Insect cell expression vector pTIE1 (others)
References: UniProt: Q5VMP0
#2: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 19004.215 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: Insect cell expression vector pTIE1 (others)
References: UniProt: Q39255

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→81.89 Å / Num. obs: 38298 / % possible obs: 94.1 % / Redundancy: 3.69 % / Net I/σ(I): 12
Reflection shellResolution: 3→3.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HZG

5hzg


Resolution: 3.01→81.89 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.814 / SU B: 22.917 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31193 1631 5 %RANDOM
Rwork0.23537 ---
obs0.23921 30772 81.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.428 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.01→81.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10174 0 0 0 10174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910370
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210021
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.97614078
X-RAY DIFFRACTIONr_angle_other_deg1.067323020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.02951281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61622.793444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.909151727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6531589
X-RAY DIFFRACTIONr_chiral_restr0.0870.21634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111475
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7546.1315178
X-RAY DIFFRACTIONr_mcbond_other3.7556.1325177
X-RAY DIFFRACTIONr_mcangle_it6.0659.1846441
X-RAY DIFFRACTIONr_mcangle_other6.0649.1846442
X-RAY DIFFRACTIONr_scbond_it3.446.4365192
X-RAY DIFFRACTIONr_scbond_other3.446.4365190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7699.5327637
X-RAY DIFFRACTIONr_long_range_B_refined9.26248.84611133
X-RAY DIFFRACTIONr_long_range_B_other9.26248.84611134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.008→3.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 73 -
Rwork0.311 1105 -
obs--40.29 %

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