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- PDB-7c96: Avr1d:GmPUB13 U-box -

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Basic information

Entry
Database: PDB / ID: 7c96
TitleAvr1d:GmPUB13 U-box
Components
  • RING-type E3 ubiquitin transferase
  • RxLR effector protein Avh6
KeywordsIMMUNE SYSTEM / Complex / Inhibitor / Self ubiquitination / negative regulatory of Plant immunity
Function / homology
Function and homology information


: / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell / cell surface receptor signaling pathway / extracellular region
Similarity search - Function
RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / U-box domain / Adaptor protein Cbl, N-terminal domain superfamily / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / U-box domain / Adaptor protein Cbl, N-terminal domain superfamily / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase / RxLR effector protein Avh6
Similarity search - Component
Biological speciesPhytophthora sojae (eukaryote)
Glycine soja (wild soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsXing, W. / Hu, Q. / Zhou, J. / Yao, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Phytophthora sojae effector Avr1d functions as an E2 competitor and inhibits ubiquitination activity of GmPUB13 to facilitate infection.
Authors: Lin, Y. / Hu, Q. / Zhou, J. / Yin, W. / Yao, D. / Shao, Y. / Zhao, Y. / Guo, B. / Xia, Y. / Chen, Q. / Wang, Y. / Ye, W. / Xie, Q. / Tyler, B.M. / Xing, W. / Wang, Y.
History
DepositionJun 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RxLR effector protein Avh6
B: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)15,4242
Polymers15,4242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-9 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.547, 69.547, 153.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein RxLR effector protein Avh6 / Avirulence homolog protein 6 / Avirulence protein 1d


Mass: 6738.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Phytophthora sojae (strain P6497) (eukaryote)
Strain: P6497 / Gene: Avh6, Avh6-1, Avr1d / Production host: Escherichia coli (E. coli) / References: UniProt: G4ZLE6
#2: Protein RING-type E3 ubiquitin transferase / Soybean U-box contained protein


Mass: 8685.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine soja (wild soybean) / Gene: D0Y65_029891 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A445I1B1, RING-type E3 ubiquitin transferase
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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: BIENCE,PEG20,000,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.51→28.76 Å / Num. obs: 14060 / % possible obs: 99.3 % / Redundancy: 10.921 % / Biso Wilson estimate: 73.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Χ2: 1.016 / Net I/σ(I): 18.81 / Num. measured all: 153546
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.51-2.669.1450.972.3820549228422470.8031.02798.4
2.66-2.8511.5820.6714.1924507211621160.9290.702100
2.85-3.0711.5090.3118.6623029200120010.9860.325100
3.07-3.3611.4250.16514.8620954183418340.9960.172100
3.36-3.7511.2090.09623.5818551165616550.9980.199.9
3.75-4.3211.1320.06132.9416464147914790.9990.064100
4.32-5.2611.2270.04942.7513876123612360.9990.051100
5.26-7.3210.8530.05242.61104519639630.9990.054100
7.32-28.769.7640.04345.3951655845290.9970.04590.6
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18_3861refinement
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→28.76 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1395 9.92 %
Rwork0.2351 12662 -
obs0.2365 14057 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.14 Å2 / Biso mean: 96.0352 Å2 / Biso min: 39.2 Å2
Refinement stepCycle: final / Resolution: 2.51→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 0 0 1010
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.60.32921420.35471233137597
2.6-2.710.34611370.334112581395100
2.71-2.830.35621380.298912861424100
2.83-2.980.30361350.274212771412100
2.98-3.170.29391360.266212881424100
3.17-3.410.26771360.244612691405100
3.41-3.750.25631490.24612711420100
3.75-4.290.24461440.229412681412100
4.29-5.40.20241410.19412821423100
5.41-28.760.2341370.2181230136797
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)
10.14790.0724-0.05250.0435-0.02550.02730.08250.12510.06980.1765-0.0501-0.04040.0925-0.0322-0.01822.81990.70260.1120.0551-0.57630.80353.6782-28.9907-13.2161
20.17810.0078-0.11820.56020.13380.3384-0.37730.392-0.2998-0.1785-0.18560.270.6994-0.0676-0.33991.850.345-0.04540.1966-0.15410.7313.6849-23.9854-4.536
30.00880.0038-0.00910.00830.00230.00340.3533-0.1264-0.01190.09880.17050.39430.0512-0.043-01.95410.42740.20481.03670.01510.986813.6241-30.30010.9621
40.3276-0.0605-0.01830.2750.30130.28980.02550.17750.1366-0.4381-0.4435-0.48580.71990.0686-0.2731.96891.00890.21580.6403-0.14150.735414.3972-23.7743-5.4535
50.0044-0.00480.0084-0.0043-0.0060.01120.0994-0.3665-0.01950.3278-0.16480.02210.0635-0.1886-00.67530.1745-0.06580.8597-0.05121.312116.9351-8.1795-4.6103
60.17630.04380.02810.0024-0.01740.0171-0.18260.80130.21460.10950.39060.12850.23270.28780.00090.79470.248-0.00080.6188-0.15560.87088.2317-9.9564-8.5856
70.161-0.1897-0.01770.2152-0.03710.0410.30.2471-0.04920.2271-0.267-0.67510.28620.0202-00.7640.0630.06180.4909-0.10510.5175-1.6813-8.9098-6.3217
80.01860.01960.03670.03880.07120.1906-0.1570.0443-0.45820.1418-0.15580.20060.1546-0.0230.00041.1163-0.33250.12910.9664-0.20390.7592-8.6383-16.5566-4.6323
90.0131-0.0272-0.01640.02670.0090.0354-0.1249-0.2639-0.22570.5095-0.08960.0460.8594-0.238100.8988-0.05840.12510.5088-0.02530.6367-4.9076-12.50342.4974
100.093-0.11340.14620.219-0.08790.21230.2238-0.02560.2652-0.218-0.1243-0.2126-0.24240.0132-00.48470.01340.06930.4889-0.14460.6379.06310.7382-6.9633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 85 )A74 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 98 )A86 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 106 )A99 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 125 )A107 - 125
5X-RAY DIFFRACTION5chain 'B' and (resid 255 through 261 )B255 - 261
6X-RAY DIFFRACTION6chain 'B' and (resid 262 through 272 )B262 - 272
7X-RAY DIFFRACTION7chain 'B' and (resid 273 through 292 )B273 - 292
8X-RAY DIFFRACTION8chain 'B' and (resid 293 through 297 )B293 - 297
9X-RAY DIFFRACTION9chain 'B' and (resid 298 through 307 )B298 - 307
10X-RAY DIFFRACTION10chain 'B' and (resid 308 through 327 )B308 - 327

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