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- PDB-8jtk: Structure of AYWB phytoplasma SAP05 recognizing AtRpn10 -

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Basic information

Entry
Database: PDB / ID: 8jtk
TitleStructure of AYWB phytoplasma SAP05 recognizing AtRpn10
Components
  • 26S proteasome non-ATPase regulatory subunit 4 homolog
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
KeywordsPLANT PROTEIN / Complex / Proteasome / Hijack
Function / homology
Function and homology information


stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / peptide receptor activity / regulation of seed germination / response to misfolded protein / leaf senescence / leaf development / pollen development ...stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / peptide receptor activity / regulation of seed germination / response to misfolded protein / leaf senescence / leaf development / pollen development / response to auxin / response to sucrose / response to abscisic acid / proteasome regulatory particle, base subcomplex / proteasome assembly / polyubiquitin modification-dependent protein binding / 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 / cytosol
Similarity search - Function
Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Sequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / 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 speciesArabidopsis thaliana (thale cress)
Aster yellows witches'-broom phytoplasma
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsDu, Y.X. / Zhang, L.Y. / Zheng, Q.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentYFC3401501 China
CitationJournal: To Be Published
Title: Structural basis for SAP05 driving ubiquitin-independent protein degradation
Authors: Zhang, L.Y. / Du, Y.X. / Zheng, Q.Y.
History
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 26S proteasome non-ATPase regulatory subunit 4 homolog
A: Sequence-variable mosaic (SVM) signal sequence domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,1912
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-8 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.240, 49.240, 215.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-258-

HOH

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Components

#1: 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: 20879.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RPN10, MBP1, MCB1, At4g38630, F20M13.190, T9A14.7 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55034
#2: Protein Sequence-variable mosaic (SVM) signal sequence domain-containing protein


Mass: 12310.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aster yellows witches'-broom phytoplasma (strain AYWB) (bacteria)
Gene: AYWB_032 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q2NK94
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.57→71.72 Å / Num. obs: 42242 / % possible obs: 95.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.021 / Rrim(I) all: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.57→1.65 Å / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6330 / CC1/2: 0.736 / Rpim(I) all: 0.314 / Rrim(I) all: 0.831 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5data processing
Aimless0.7.7data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→24.93 Å / SU ML: 0.1964 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.9635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 2039 4.84 %
Rwork0.187 40103 -
obs0.1883 42142 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 1.57→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 200 2522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762361
X-RAY DIFFRACTIONf_angle_d1.0333192
X-RAY DIFFRACTIONf_chiral_restr0.066361
X-RAY DIFFRACTIONf_plane_restr0.0086419
X-RAY DIFFRACTIONf_dihedral_angle_d15.8595887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.32121620.27722724X-RAY DIFFRACTION99.9
1.6-1.640.33141510.26792748X-RAY DIFFRACTION99.83
1.64-1.690.32031480.25662687X-RAY DIFFRACTION100
1.69-1.740.28961560.25422732X-RAY DIFFRACTION100
1.74-1.790.25591190.23742735X-RAY DIFFRACTION99.96
1.79-1.860.23561460.20952768X-RAY DIFFRACTION100
1.86-1.930.3215690.2151566X-RAY DIFFRACTION56.91
1.93-2.020.21691070.20852429X-RAY DIFFRACTION87.84
2.02-2.130.23241420.20522806X-RAY DIFFRACTION100
2.13-2.260.23861270.18782590X-RAY DIFFRACTION93.37
2.26-2.430.21721550.18582765X-RAY DIFFRACTION100
2.43-2.680.2281540.20122793X-RAY DIFFRACTION100
2.68-3.060.23041230.18952862X-RAY DIFFRACTION99.93
3.06-3.860.18961510.17492851X-RAY DIFFRACTION100
3.86-24.930.17711290.16113047X-RAY DIFFRACTION99.22

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