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- PDB-8j4b: Crystal structure of OY phytoplasma SAP05 in complex with AtSPL13 -

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Basic information

Entry
Database: PDB / ID: 8j4b
TitleCrystal structure of OY phytoplasma SAP05 in complex with AtSPL13
Components
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
  • Squamosa promoter-binding-like protein 13A
KeywordsPLANT PROTEIN / ubiquitin-independent protein degradation
Function / homology
Function and homology information


anther development / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus
Similarity search - Function
SBP domain / SBP domain superfamily / Squamosa promoter-binding-like protein / SBP domain / Zinc finger SBP-type profile. / Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence
Similarity search - Domain/homology
Squamosa promoter-binding-like protein 13A / Sequence-variable mosaic (SVM) signal sequence domain-containing protein
Similarity search - Component
Biological speciesOnion yellows phytoplasma OY-M (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDong, C. / Yan, X. / Yuan, X.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32271265 China
National Natural Science Foundation of China (NSFC)32071193 China
National Natural Science Foundation of China (NSFC)81874039 China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors.
Authors: Yan, X. / Yuan, X. / Lv, J. / Zhang, B. / Huang, Y. / Li, Q. / Ma, J. / Li, Y. / Wang, X. / Li, Y. / Yu, Y. / Liu, Q. / Liu, T. / Mi, W. / Dong, C.
History
DepositionApr 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
C: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
B: Squamosa promoter-binding-like protein 13A
D: Squamosa promoter-binding-like protein 13A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2138
Polymers39,9514
Non-polymers2624
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-5 kcal/mol
Surface area17040 Å2
Unit cell
Length a, b, c (Å)90.920, 63.350, 68.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Sequence-variable mosaic (SVM) signal sequence domain-containing protein / OY-M SAP05


Mass: 12288.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onion yellows phytoplasma OY-M (bacteria)
Strain: OY-M / Gene: PAM_518 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6YQ57
#2: Protein Squamosa promoter-binding-like protein 13A / AtSPL13


Mass: 7686.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPL13A, SPL13 / Production host: Escherichia coli (E. coli) / References: UniProt: B9DI20
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.2828 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 2→36.93 Å / Num. obs: 27306 / % possible obs: 99.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 26.88 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.74
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.21 / Num. unique obs: 2608 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.93 Å / SU ML: 0.2343 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1409 5.16 %
Rwork0.1751 25897 -
obs0.1771 27306 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.09 Å2
Refinement stepCycle: LAST / Resolution: 2→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 4 284 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862815
X-RAY DIFFRACTIONf_angle_d0.92653784
X-RAY DIFFRACTIONf_chiral_restr0.0545377
X-RAY DIFFRACTIONf_plane_restr0.0054504
X-RAY DIFFRACTIONf_dihedral_angle_d5.8764360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.28641460.19942463X-RAY DIFFRACTION96.74
2.07-2.150.19751270.18852540X-RAY DIFFRACTION99.59
2.15-2.250.25191280.17672573X-RAY DIFFRACTION99.85
2.25-2.370.22981240.18642591X-RAY DIFFRACTION99.89
2.37-2.520.22951170.18962597X-RAY DIFFRACTION99.93
2.52-2.710.25521320.19722577X-RAY DIFFRACTION99.96
2.71-2.990.24171500.18972590X-RAY DIFFRACTION100
2.99-3.420.22911590.17642585X-RAY DIFFRACTION99.96
3.42-4.310.18111540.15292640X-RAY DIFFRACTION99.96
4.31-36.930.1861720.16612741X-RAY DIFFRACTION99.79

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