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- PDB-8j48: Crystal structure of OY phytoplasma SAP05 in complex with AtGATA18 -

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Basic information

Entry
Database: PDB / ID: 8j48
TitleCrystal structure of OY phytoplasma SAP05 in complex with AtGATA18
Components
  • GATA transcription factor 18
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
KeywordsPLANT PROTEIN / ubiquitin-independent protein degradation
Function / homology
Function and homology information


cotyledon development / regulation of meristem structural organization / regulation of flower development / flower development / embryo development ending in seed dormancy / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription ...cotyledon development / regulation of meristem structural organization / regulation of flower development / flower development / embryo development ending in seed dormancy / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding / nucleus
Similarity search - Function
GATA transcription factor 18/19/20 / Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Sequence-variable mosaic (SVM) signal sequence domain-containing protein / GATA transcription factor 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Onion yellows phytoplasma OY-M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 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
D: GATA transcription factor 18
B: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
A: GATA transcription factor 18
C: Sequence-variable mosaic (SVM) signal sequence domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0356
Polymers35,9044
Non-polymers1312
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-8 kcal/mol
Surface area14490 Å2
Unit cell
Length a, b, c (Å)35.835, 73.397, 58.671
Angle α, β, γ (deg.)90.00, 107.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GATA transcription factor 18 / AtGATA18


Mass: 5663.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GATA18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LC79
#2: Protein Sequence-variable mosaic (SVM) signal sequence domain-containing protein


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
#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.: 187 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium acetate dihydrate, 20% (wt/vol) 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: 1.94→36.7 Å / Num. obs: 20865 / % possible obs: 97.23 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.79
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 1.006 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 1747

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→36.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2365 --
Rwork0.2021 --
obs-20846 81.6 %
Refinement stepCycle: LAST / Resolution: 1.94→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 2 187 2456

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