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- PDB-6bro: Crystal structure of ASK1-D3 ubiquitin ligase form1 -

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Basic information

Entry
Database: PDB / ID: 6bro
TitleCrystal structure of ASK1-D3 ubiquitin ligase form1
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-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / response to light stimulus / chromosome segregation / spindle / microtubule cytoskeleton organization / 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 / 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: 2.5 Å
AuthorsShabek, N. / Zheng, N.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water8,395466
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-25 kcal/mol
Surface area33000 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-26 kcal/mol
Surface area33570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.728, 79.730, 153.437
Angle α, β, γ (deg.)90.000, 128.590, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUBA5 - 6965 - 664
21GLUGLULEULEUDC5 - 6965 - 664
12LEULEUGLUGLUAB8 - 1608 - 160
22LEULEUGLUGLUCD8 - 1608 - 160

NCS ensembles :
ID
1
2

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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


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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 6.5% CP-42; 175 mM Sodium Citrate tribasic dihydrate; 87 mM HEPES sodium pH 7.5; 26% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→119.93 Å / Num. obs: 75576 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rsym value: 0.126 / Net I/σ(I): 35.5
Reflection shellResolution: 2.5→2.59 Å / Num. unique all: 3332 / Rsym value: 0.403

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.5→119.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.074 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.242
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 3700 4.9 %RANDOM
Rwork0.2018 ---
obs0.2034 71877 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.59 Å2 / Biso mean: 39.15 Å2 / Biso min: 11.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.07 Å2
2---1.14 Å20 Å2
3---0.98 Å2
Refinement stepCycle: final / Resolution: 2.5→119.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11366 0 0 466 11832
Biso mean---34.87 -
Num. residues----1458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911600
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.97815748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23651435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33623.044496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.722151943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6361599
X-RAY DIFFRACTIONr_chiral_restr0.0970.21836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218641
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B376540.05
12D376540.05
21A65960.08
22C65960.08
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 236 -
Rwork0.26 4682 -
all-4918 -
obs--87.04 %
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)
10.2933-0.04770.16020.56490.10760.1247-0.00840.0277-0.0122-0.03670.0076-0.0646-0.02830.0140.00070.064-0.0058-0.09250.01640.00390.1638-35.468536.60733.4285
21.28771.0333-0.8281.8783-1.20273.72720.2411-0.2662-0.1050.3929-0.1324-0.3342-0.34690.0228-0.10860.1444-0.0219-0.12630.06650.00310.1798-43.68157.852120.1366
30.19120.14350.20420.5679-0.01690.2844-0.02630.023-0.0395-0.06230.0405-0.0513-0.03350.0165-0.01430.1378-0.009-0.11460.004-0.00240.12353.9097-3.96137.8375
43.5883-0.8913-1.03271.95571.27621.2759-0.2619-0.1111-0.2579-0.3846-0.12930.5038-0.122-0.17890.39120.20030.0204-0.15420.0557-0.03790.229-11.288124.682947.9096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 697
2X-RAY DIFFRACTION2A8 - 160
3X-RAY DIFFRACTION3D5 - 696
4X-RAY DIFFRACTION4C6 - 160

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