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- PDB-8j4a: Crystal structure of OY phytoplasma SAP05 in complex with AtRPN10 -

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Basic information

Entry
Database: PDB / ID: 8j4a
TitleCrystal structure of OY phytoplasma SAP05 in complex with AtRPN10
Components
  • 26S proteasome non-ATPase regulatory subunit 4 homolog
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
KeywordsPLANT PROTEIN / ubiquitin-independent protein degradation
Function / homology
Function and homology information


stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / response to misfolded protein / leaf senescence / peptide receptor activity / regulation of seed germination / leaf development / pollen development ...stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / response to misfolded protein / leaf senescence / peptide receptor activity / regulation of seed germination / leaf development / pollen development / response to auxin / response to sucrose / response to abscisic acid / polyubiquitin modification-dependent protein binding / proteasome assembly / response to salt stress / proteasome complex / protein catabolic process / response to heat / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA damage response / nucleus / plasma membrane
Similarity search - Function
Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / VWFA domain profile. ...Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4 homolog / 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 / MOLECULAR REPLACEMENT / Resolution: 1.97 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
D: 26S proteasome non-ATPase regulatory subunit 4 homolog
B: 26S proteasome non-ATPase regulatory subunit 4 homolog


Theoretical massNumber of molelcules
Total (without water)66,4054
Polymers66,4054
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-15 kcal/mol
Surface area23830 Å2
Unit cell
Length a, b, c (Å)54.045, 40.586, 130.329
Angle α, β, γ (deg.)90.000, 93.013, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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 26S proteasome non-ATPase regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN10 / AtRPN10 / 26S proteasome regulatory subunit S5A homolog / ...26S proteasome regulatory subunit RPN10 / AtRPN10 / 26S proteasome regulatory subunit S5A homolog / Multiubiquitin chain-binding protein 1 / AtMCB1


Mass: 20913.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RPN10, MBP1, MCB1, At4g38630, F20M13.190, T9A14.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P55034
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium acetate dehydrate, 18% PEG3350, 0.1 M Guanine hydrochloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.97→48.95 Å / Num. obs: 38214 / % possible obs: 94.58 % / Redundancy: 2.8 % / Biso Wilson estimate: 5.74 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.87
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.4679 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 3983

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→48.95 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 1833 4.8 %
Rwork0.1925 36371 -
obs0.1954 38204 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.23 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 0 477 5073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764676
X-RAY DIFFRACTIONf_angle_d0.96936320
X-RAY DIFFRACTIONf_chiral_restr0.0555708
X-RAY DIFFRACTIONf_plane_restr0.0051830
X-RAY DIFFRACTIONf_dihedral_angle_d5.9808618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.3111410.24492932X-RAY DIFFRACTION98.05
2.03-2.090.3011030.2222153X-RAY DIFFRACTION74.31
2.09-2.150.30181520.20862881X-RAY DIFFRACTION98.16
2.15-2.230.24591380.20852887X-RAY DIFFRACTION98.21
2.23-2.320.26221720.20592867X-RAY DIFFRACTION98.8
2.32-2.430.27811430.20242882X-RAY DIFFRACTION98.5
2.43-2.550.26691280.19652915X-RAY DIFFRACTION98.42
2.55-2.710.27681340.20352608X-RAY DIFFRACTION87.69
2.71-2.920.26691320.20192868X-RAY DIFFRACTION97.98
2.92-3.220.27421450.19672883X-RAY DIFFRACTION97.46
3.22-3.680.23421340.16852575X-RAY DIFFRACTION86.83
3.68-4.640.17021660.14982902X-RAY DIFFRACTION97.68
4.64-48.950.22931450.1723018X-RAY DIFFRACTION97.35

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