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- PDB-8j49: Crystal structure of OY phytoplasma SAP05 in complex with AtSPL5 -

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Basic information

Entry
Database: PDB / ID: 8j49
TitleCrystal structure of OY phytoplasma SAP05 in complex with AtSPL5
Components
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
  • Squamosa promoter-binding-like protein 5
KeywordsPLANT PROTEIN / ubiquitin-independent proteasomal degradation
Function / homology
Function and homology information


regulation of vegetative phase change / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Squamosa promoter-binding-like protein / SBP domain / SBP domain superfamily / SBP domain / Zinc finger SBP-type profile. / Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence
Similarity search - Domain/homology
Sequence-variable mosaic (SVM) signal sequence domain-containing protein / Squamosa promoter-binding-like protein 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Onion yellows phytoplasma OY-M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsDong, C. / Yan, X. / Yuan, X.
Funding support China, 3items
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
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: Squamosa promoter-binding-like protein 5
B: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
D: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6855
Polymers31,5543
Non-polymers1312
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-5 kcal/mol
Surface area13630 Å2
Unit cell
Length a, b, c (Å)30.159, 45.091, 52.947
Angle α, β, γ (deg.)92.43, 101.86, 108.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Squamosa promoter-binding-like protein 5


Mass: 7703.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPL5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S758
#2: Protein Sequence-variable mosaic (SVM) signal sequence domain-containing protein


Mass: 11925.320 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium fluoride, 20% 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: 1.28277 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28277 Å / Relative weight: 1
ReflectionResolution: 1.66→42.44 Å / Num. obs: 25490 / % possible obs: 83.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 11.7
Reflection shellResolution: 1.66→1.75 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1455

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→42.44 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 28.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2197 1909 7.94 %
Rwork0.1919 --
obs0.1941 24051 78.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 2 191 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072234
X-RAY DIFFRACTIONf_angle_d0.973009
X-RAY DIFFRACTIONf_dihedral_angle_d6.445290
X-RAY DIFFRACTIONf_chiral_restr0.06302
X-RAY DIFFRACTIONf_plane_restr0.01401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.3041510.2283645X-RAY DIFFRACTION32
1.7-1.740.2469400.2401419X-RAY DIFFRACTION21
1.74-1.80.2771040.21341153X-RAY DIFFRACTION58
1.8-1.850.2731460.22611610X-RAY DIFFRACTION81
1.85-1.920.2391340.24271624X-RAY DIFFRACTION81
1.92-20.20811570.20481708X-RAY DIFFRACTION85
2-2.090.27461350.20991750X-RAY DIFFRACTION88
2.09-2.20.22211660.20091839X-RAY DIFFRACTION92
2.2-2.340.24151460.20641821X-RAY DIFFRACTION89
2.34-2.520.25381690.20481907X-RAY DIFFRACTION94
2.52-2.770.23941660.21141884X-RAY DIFFRACTION95
2.77-3.170.23211580.19681910X-RAY DIFFRACTION96
3.17-3.990.19691740.16911933X-RAY DIFFRACTION96
3.99-42.440.17841630.16541939X-RAY DIFFRACTION96

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