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- PDB-8jtl: Structure of OY phytoplasma SAP05 binding with AtRpn10 -

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Basic information

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


stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / regulation of seed germination / peptide receptor activity / response to misfolded protein / leaf senescence / leaf development / pollen development ...stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / regulation of seed germination / peptide receptor activity / 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)
Onion yellows phytoplasma
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDu, Y.X. / Zhang, L.Y. / Zheng, Q.Y.
Funding support1items
OrganizationGrant numberCountry
Other governmentYFC3401501
CitationJournal: Iscience / Year: 2024
Title: Structure basis for recognition of plant Rpn10 by phytoplasma SAP05 in ubiquitin-independent protein degradation.
Authors: Zhang, L. / Du, Y. / Qu, Q. / Zheng, Q.
History
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,5314
Polymers66,5314
Non-polymers00
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-17 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.410, 39.370, 121.940
Angle α, β, γ (deg.)90.000, 93.790, 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 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.: 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 / 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: 12385.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onion yellows phytoplasma (strain OY-M) (bacteria)
Gene: PAM_518 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6YQ57
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 15% w/v PEG 6000, 5% v/v MPD, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.69→31.08 Å / Num. obs: 55704 / % possible obs: 99.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.06 Å2 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.074 / Rrim(I) all: 0.185 / Net I/σ(I): 5
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 1.773 / Mean I/σ(I) obs: 1 / Num. unique obs: 4021 / Rpim(I) all: 0.763 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→25.35 Å / SU ML: 0.2084 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 2369 4.98 %
Rwork0.184 45164 -
obs0.1857 47533 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.08 Å2
Refinement stepCycle: LAST / Resolution: 1.78→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 0 410 5062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01394738
X-RAY DIFFRACTIONf_angle_d1.35576408
X-RAY DIFFRACTIONf_chiral_restr0.0737716
X-RAY DIFFRACTIONf_plane_restr0.0097842
X-RAY DIFFRACTIONf_dihedral_angle_d15.79881776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.31541320.30942619X-RAY DIFFRACTION97.94
1.82-1.860.35541320.27142610X-RAY DIFFRACTION98.21
1.86-1.90.27991530.26192592X-RAY DIFFRACTION98.53
1.9-1.950.28081470.24172625X-RAY DIFFRACTION98.37
1.95-20.23761420.21652641X-RAY DIFFRACTION98.41
2-2.060.24371310.21452645X-RAY DIFFRACTION98.54
2.06-2.120.24791390.21562607X-RAY DIFFRACTION98.56
2.12-2.20.25491430.19932667X-RAY DIFFRACTION98.39
2.2-2.290.2631510.19322612X-RAY DIFFRACTION98.71
2.29-2.390.23741250.18922659X-RAY DIFFRACTION98.79
2.39-2.520.23851570.18792637X-RAY DIFFRACTION98.9
2.52-2.680.25031470.18712640X-RAY DIFFRACTION99.18
2.68-2.880.22721090.18162723X-RAY DIFFRACTION99.37
2.88-3.170.19691240.17452686X-RAY DIFFRACTION99.15
3.17-3.630.20831540.16372708X-RAY DIFFRACTION99.31
3.63-4.570.17611360.14832706X-RAY DIFFRACTION99.37
4.57-25.350.19281470.18382787X-RAY DIFFRACTION98.16
Refinement TLS params.Method: refined / Origin x: -27.147677524 Å / Origin y: 2.91022654876 Å / Origin z: 29.838573796 Å
111213212223313233
T0.211524501324 Å2-0.0119894572072 Å20.0248078312268 Å2-0.18022472185 Å2-0.00261011888198 Å2--0.212820963637 Å2
L0.896818322864 °2-0.33465137425 °20.696066773215 °2-0.723225782417 °2-0.353738520803 °2--1.06081530267 °2
S0.0477215301509 Å °-0.0611424580013 Å °0.00414160739826 Å °-0.149985399554 Å °-0.0367359242305 Å °0.0196182432624 Å °0.0792860877162 Å °0.0109161491225 Å °-0.00195516404097 Å °
Refinement TLS groupSelection details: all

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