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- PDB-6lhn: RLGSGG-AtPRT6 UBR box -

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Basic information

Entry
Database: PDB / ID: 6lhn
TitleRLGSGG-AtPRT6 UBR box
ComponentsE3 ubiquitin-protein ligase PRT6
KeywordsLIGASE / PRT6 / Arabidopsis thaliana
Function / homology
Function and homology information


regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / defense response to bacterium ...regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / defense response to bacterium / protein ubiquitination / zinc ion binding
Similarity search - Function
E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway ...E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PRT6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, L. / Kwon, D.H. / Song, H.K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.
Authors: Kim, L. / Kwon, D.H. / Heo, J. / Park, M.R. / Song, H.K.
History
DepositionDec 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase PRT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3864
Polymers8,1901
Non-polymers1963
Water00
1
A: E3 ubiquitin-protein ligase PRT6
hetero molecules

A: E3 ubiquitin-protein ligase PRT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7728
Polymers16,3802
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_445z-1/4,-y-1/4,x+1/41
Buried area1400 Å2
ΔGint-4 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.414, 95.414, 95.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein E3 ubiquitin-protein ligase PRT6 / Protein GREENING AFTER EXTENDED DARKNESS 1 / Protein PROTEOLYSIS 6 / RING-type E3 ubiquitin transferase PRT6


Mass: 8189.965 Da / Num. of mol.: 1 / Fragment: UBR box
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60
Production host: Escherichia coli (E. coli)
References: UniProt: F4KCC2, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.45 Å3/Da / Density % sol: 72.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium sulfate, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.499→42.67 Å / Num. obs: 5522 / % possible obs: 99.48 % / Redundancy: 9 % / CC1/2: 0.986 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 5513 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KGG

6kgg
PDB Unreleased entry


Resolution: 2.5→38.95 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 23.4
RfactorNum. reflection% reflection
Rfree0.2503 553 10.01 %
Rwork0.2127 --
obs0.2164 5522 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 0 3 0 565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012576
X-RAY DIFFRACTIONf_angle_d1.242780
X-RAY DIFFRACTIONf_dihedral_angle_d10.762326
X-RAY DIFFRACTIONf_chiral_restr0.05876
X-RAY DIFFRACTIONf_plane_restr0.008107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75020.28831340.24861204X-RAY DIFFRACTION100
2.7502-3.14810.31071340.23811207X-RAY DIFFRACTION100
3.1481-3.96580.25141380.20381239X-RAY DIFFRACTION99
3.9658-38.950.22291470.20211319X-RAY DIFFRACTION99

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