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- PDB-8pfd: Crystal structure of binary complex between Aster yellows witches... -

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Basic information

Entry
Database: PDB / ID: 8pfd
TitleCrystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana
Components
  • 26S proteasome non-ATPase regulatory subunit 4 homolog
  • Sequence-variable mosaic (SVM) signal sequence domain-containing protein
KeywordsPROTEIN BINDING / Targeted protein degradation / ubiquitin-independent / bacterial effector protein / 26S proteasome
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 speciesAster yellows witches'-broom phytoplasma AYWB (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHuang, W. / Liu, Q. / Maqbool, A. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Hogenhout, S.A.
Funding support France, United Kingdom, 4items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0024/2015 France
Engineering and Physical Sciences Research CouncilEP/X024415/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9797 United Kingdom
John Innes FoundationNone United Kingdom
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation.
Authors: Liu, Q. / Maqbool, A. / Mirkin, F.G. / Singh, Y. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Huang, W. / Hogenhout, S.A.
#1: Journal: Biorxiv / Year: 2023
Title: Bimodular architecture of bacterial effector SAP05 drives ubiquitin-independent targeted protein degradation
Authors: Liu, Q. / Maqbool, A. / Mirkin, F.G. / Singh, Y. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Huang, W. / Hogenhout, S.A.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.entity_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,1912
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-9 kcal/mol
Surface area12980 Å2
Unit cell
Length a, b, c (Å)42.391, 68.599, 49.851
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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
Details: The crystallized sequence corresponds to residues 33-135 of the full 135-residue wild-type sequence, which is prepended by a GLY-PRO dipeptide left over from cleavage of the affinity tag.
Source: (gene. exp.) Aster yellows witches'-broom phytoplasma AYWB (bacteria)
Gene: AYWB_032 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2NK94
#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: 20879.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The crystallized sequence corresponds to residues 2-193 of the full 386-residue wild-type sequence. The native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RPN10, MBP1, MCB1, At4g38630, F20M13.190, T9A14.7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55034
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.17→68.6 Å / Num. obs: 15199 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.122 / Χ2: 0.94 / Net I/σ(I): 10.9 / Num. measured all: 210355
Reflection shellResolution: 2.17→2.24 Å / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.599 / Num. measured all: 18117 / Num. unique obs: 1337 / CC1/2: 0.436 / Rpim(I) all: 0.729 / Rrim(I) all: 2.7 / Χ2: 0.93 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→49.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 18.297 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25225 697 4.6 %RANDOM
Rwork0.19791 ---
obs0.20035 14486 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.42 Å2
2---1.29 Å2-0 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.17→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 30 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132235
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172165
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6383021
X-RAY DIFFRACTIONr_angle_other_deg1.1841.5854972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5585281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89124.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30215394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3471510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5094.1451136
X-RAY DIFFRACTIONr_mcbond_other1.5094.1441135
X-RAY DIFFRACTIONr_mcangle_it2.2856.2091413
X-RAY DIFFRACTIONr_mcangle_other2.2856.211414
X-RAY DIFFRACTIONr_scbond_it1.5124.2891099
X-RAY DIFFRACTIONr_scbond_other1.5124.291100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4276.3781609
X-RAY DIFFRACTIONr_long_range_B_refined4.39849.1212400
X-RAY DIFFRACTIONr_long_range_B_other4.39649.112399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.227 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 43 -
Rwork0.314 1076 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2866-2.25750.84577.3183-0.5824.8428-0.2078-0.28460.24190.47120.0469-0.4222-0.20470.05580.16080.0431-0.0288-0.02780.2157-0.04040.03584.74315.499.96
22.8105-1.16650.2356.3443-0.12921.5317-0.1254-0.351-0.09490.69990.1428-0.24620.07010.1567-0.01740.08310.0423-0.02690.29660.02460.01814.093-11.55911.076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 133
2X-RAY DIFFRACTION2B1 - 192

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