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- PDB-8zga: F-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 8zga
TitleF-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
ComponentsF-degron,E3 ubiquitin-protein ligase PRT1
KeywordsLIGASE / complex / ZZ-domain / Arabidopsis thaliana / PRT1 / E3-ubiquitin ligase
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the N-end rule pathway / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PRT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, W.S. / Song, H.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C3008285 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4030068 Korea, Republic Of
National Research Foundation (NRF, Korea)2022M3A9G8082638 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin.
Authors: Yang, W.S. / Kim, S.H. / Kim, M. / Shin, H. / Lee, J. / Sandmann, A. / Park, O.K. / Dissmeyer, N. / Song, H.K.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: 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

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Assembly

Deposited unit
A: F-degron,E3 ubiquitin-protein ligase PRT1
B: F-degron,E3 ubiquitin-protein ligase PRT1
C: F-degron,E3 ubiquitin-protein ligase PRT1
D: F-degron,E3 ubiquitin-protein ligase PRT1
E: F-degron,E3 ubiquitin-protein ligase PRT1
F: F-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,89020
Polymers47,0576
Non-polymers83414
Water23413
1
A: F-degron,E3 ubiquitin-protein ligase PRT1
E: F-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9727
Polymers15,6862
Non-polymers2865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area8180 Å2
MethodPISA
2
B: F-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules

D: F-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9727
Polymers15,6862
Non-polymers2865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1620 Å2
ΔGint-13 kcal/mol
Surface area8430 Å2
MethodPISA
3
C: F-degron,E3 ubiquitin-protein ligase PRT1
F: F-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9476
Polymers15,6862
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-9 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.729, 86.439, 89.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
F-degron,E3 ubiquitin-protein ligase PRT1 / Proteolysis 1 protein / RING-type E3 ubiquitin transferase PRT1


Mass: 7842.824 Da / Num. of mol.: 6 / Fragment: ZZ-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRT1, At3g24800, K7P8.9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8LBL5, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Divalents Buffer System 2 pH 7.5 Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.1→42.83 Å / Num. obs: 22752 / % possible obs: 99.67 % / Redundancy: 14 % / Biso Wilson estimate: 51.42 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.04898 / Rrim(I) all: 0.181 / Net I/σ(I): 11.57
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 2.578 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2193 / CC1/2: 0.709 / Rpim(I) all: 0.7054 / Rrim(I) all: 2.675

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZG8

8zg8


Resolution: 2.1→42.83 Å / SU ML: 0.3826 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2945 3736 8.75 %
Rwork0.2572 38941 -
obs0.2605 22752 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 14 13 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453310
X-RAY DIFFRACTIONf_angle_d0.64284443
X-RAY DIFFRACTIONf_chiral_restr0.0437426
X-RAY DIFFRACTIONf_plane_restr0.0038601
X-RAY DIFFRACTIONf_dihedral_angle_d24.19351237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.52441020.47511248X-RAY DIFFRACTION84.53
2.12-2.150.50331570.4631397X-RAY DIFFRACTION99.68
2.15-2.180.4681160.45051486X-RAY DIFFRACTION99.94
2.18-2.210.49481410.43231482X-RAY DIFFRACTION100
2.21-2.240.49411490.42651449X-RAY DIFFRACTION100
2.24-2.280.44781330.41961421X-RAY DIFFRACTION99.87
2.28-2.320.41571460.40811475X-RAY DIFFRACTION99.63
2.32-2.360.40811220.40651462X-RAY DIFFRACTION99.87
2.36-2.40.46891450.39441413X-RAY DIFFRACTION99.81
2.4-2.450.43211390.37841467X-RAY DIFFRACTION99.75
2.45-2.50.37921350.33461460X-RAY DIFFRACTION100
2.5-2.550.43561370.33221465X-RAY DIFFRACTION99.88
2.55-2.610.33911380.32531438X-RAY DIFFRACTION99.87
2.61-2.670.32851420.28161450X-RAY DIFFRACTION100
2.67-2.750.28151340.28511431X-RAY DIFFRACTION99.81
2.75-2.830.29931460.27721467X-RAY DIFFRACTION99.75
2.83-2.920.33621500.28311428X-RAY DIFFRACTION99.94
2.92-3.020.31861360.29021444X-RAY DIFFRACTION100
3.02-3.140.36231470.27931435X-RAY DIFFRACTION99.94
3.14-3.290.33921340.28971471X-RAY DIFFRACTION99.94
3.29-3.460.2691450.25841466X-RAY DIFFRACTION99.88
3.46-3.680.37271360.26241442X-RAY DIFFRACTION100
3.68-3.960.29211420.23211448X-RAY DIFFRACTION99.94
3.96-4.360.22061470.2051446X-RAY DIFFRACTION99.87
4.36-4.990.19351430.18811446X-RAY DIFFRACTION99.94
4.99-6.280.21121350.19961448X-RAY DIFFRACTION99.87
6.29-42.830.25351390.20621456X-RAY DIFFRACTION99.87

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