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- PDB-8zgb: W-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 8zgb
TitleW-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
ComponentsW-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-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / 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-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / 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: 2.785 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: To Be Published
Title: Structural basis for the recognition of type-2 N-degron by PRT1 plant N-recognin
Authors: Yang, W.S. / Song, H.K.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: W-degron,E3 ubiquitin-protein ligase PRT1
B: W-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8537
Polymers15,4952
Non-polymers3585
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.260, 106.260, 97.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 298 through 329 or resid 331 through 346 or resid 348 through 401))
d_2ens_1(chain "B" and (resid 298 through 329 or resid 331 through 346 or resid 348 through 401))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TRPTRPCYSCYSAA298 - 3291 - 32
d_12GLUGLUSERSERAA331 - 34634 - 49
d_13VALVALALAALAAA348 - 36551 - 68
d_14ZNZNZNZNAC401
d_21TRPTRPCYSCYSBB298 - 3291 - 32
d_22GLUGLUSERSERBB331 - 34634 - 49
d_23VALVALALAALABB348 - 36551 - 68
d_24ZNZNZNZNBF401

NCS oper: (Code: givenMatrix: (0.125382589239, 0.456889591042, -0.880642440445), (0.447875221916, -0.818116809993, -0.360683615931), (-0.885260973899, -0.349194482781, -0.307207130916)Vector: 26. ...NCS oper: (Code: given
Matrix: (0.125382589239, 0.456889591042, -0.880642440445), (0.447875221916, -0.818116809993, -0.360683615931), (-0.885260973899, -0.349194482781, -0.307207130916)
Vector: 26.8900655791, 68.7388382892, 70.6104951012)

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Components

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


Mass: 7747.663 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 4.42 Å3/Da / Density % sol: 72.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 400 Tris base/ Hydrochloric acid pH 8.5 Lithium sulfate

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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: 2.785→40.77 Å / Num. obs: 7204 / % possible obs: 99.56 % / Redundancy: 28.8 % / Biso Wilson estimate: 129.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1262 / Rpim(I) all: 0.02445 / Rrim(I) all: 0.1287 / Net I/σ(I): 18.48
Reflection shellResolution: 2.785→2.884 Å / Rmerge(I) obs: 2.093 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 683 / CC1/2: 0.643 / Rpim(I) all: 0.3918 / Rrim(I) all: 2.131

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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: 2.785→40.77 Å / SU ML: 0.4761 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.6713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2613 1325 10 %
Rwork0.2345 11923 -
obs0.2373 7204 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.49 Å2
Refinement stepCycle: LAST / Resolution: 2.785→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 9 0 1059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771082
X-RAY DIFFRACTIONf_angle_d0.94481464
X-RAY DIFFRACTIONf_chiral_restr0.0553142
X-RAY DIFFRACTIONf_plane_restr0.0064198
X-RAY DIFFRACTIONf_dihedral_angle_d23.9525390
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.44159167577 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.785-2.90.46671420.46381278X-RAY DIFFRACTION96.27
2.9-3.030.34751460.39671323X-RAY DIFFRACTION100
3.03-3.190.35181480.3321333X-RAY DIFFRACTION100
3.19-3.390.30131480.33941315X-RAY DIFFRACTION100
3.39-3.650.3641500.29291347X-RAY DIFFRACTION100
3.65-4.020.31591460.27341314X-RAY DIFFRACTION100
4.02-4.60.25941440.2191346X-RAY DIFFRACTION100
4.6-5.780.21211470.20131328X-RAY DIFFRACTION100
5.79-40.770.24121540.20521339X-RAY DIFFRACTION99.87
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)
16.58487757053-0.3505592950952.612384719794.62911532007-1.717919695519.32212828348-0.2706446502431.48772322974-0.529690140646-0.2245066695960.08935469507490.6732042298730.04002562368381.319681687650.2564296354081.34970636453-0.202841465939-0.1071953577970.9112637235760.01718211396461.0146015627950.885864712742.67849117439.54600703396
23.6685962532.03081334688-2.569001736715.535701500523.402484723836.64852176145-0.008218769089660.42453395430.205259836685-0.4564560594680.2467315126220.6122412005510.464268411727-1.456748081660.3425936564931.233024630160.02181765220460.04876952569141.081739036610.1307083095191.237887510947.709167358542.467690484519.544111946
32.89783333107-1.971843922870.5623057445719.087461897220.7773497868878.080440873560.979838027619-0.557068230884-0.02511193983640.4039012319690.0928527239141-0.6379215050423.49788394645-0.5151400120890.2319900538891.794919294410.2067172222450.2339120086071.128954330230.3493594398071.1251682139352.612734877433.811538337717.81289474
48.640270331361.215546241141.963379708252.017880092283.488897319866.91216988055-0.893451840876-1.560916413-0.1521976064881.264889925480.2187677622350.526192405020.189928049092-0.4205167931410.2128426518141.49005404942-0.199450905426-0.1324890072591.344023585010.05937339091191.2053058715351.801416729139.905899080425.774258455
51.150902480970.4980662666992.132131093310.6249533926252.583443457075.05754935776-0.421592745001-1.469755311370.2804351944670.1508718388630.393465518359-0.193870029785-0.24684304665-1.73094461717-0.4421479620950.967384828576-0.0134723681642-0.1540677902561.039867275450.1370534216941.1105356820744.831596314352.93784093588.02336268757
69.334813224323.9921214275-1.31882477524.00030953554-0.2926012301387.15161770808-0.0269618783907-0.348580674355-0.0656489009840.720507354492-0.166039083654-0.264216166131-0.192811387701-0.5804348386510.04534262531820.887390644456-0.0827271124347-0.07795750126151.240414075440.09460790456920.92482961606935.158449658751.24292927137.44059674118
77.253487471171.113538098442.301620209797.865309505876.42728093955.535261016862.030799848492.207153536583.00212356417-2.69277699077-4.49699328631-5.78295999443-1.66749450981-2.026523808251.260283501382.09393091388-0.223114114122-0.5907473137321.912451373980.3029316415382.074843193528.574209226260.2526408362-1.51582046889
89.1094710048-3.255693147715.820677963733.478901087080.4458206802146.28451571674-0.4739935799491.446815239180.844149521763-0.0411225972472-0.128792426142.29540406393-1.05565518042-2.330632837940.5992094373451.1298419049-0.257351838701-0.09257367940361.7733401150.1640056910161.1285487527428.120293032448.45488380163.44133052175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 298 through 317 )AA298 - 3171 - 20
22chain 'A' and (resid 318 through 335 )AA318 - 33521 - 38
33chain 'A' and (resid 336 through 343 )AA336 - 34339 - 46
44chain 'A' and (resid 344 through 365 )AA344 - 36547 - 68
55chain 'B' and (resid 298 through 317 )BD298 - 3171 - 20
66chain 'B' and (resid 318 through 343 )BD318 - 34321 - 46
77chain 'B' and (resid 344 through 348 )BD344 - 34847 - 51
88chain 'B' and (resid 349 through 365 )BD349 - 36552 - 68

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