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- PDB-3tl8: The AvrPtoB-BAK1 complex reveals two structurally similar kinasei... -

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Basic information

Entry
Database: PDB / ID: 3tl8
TitleThe AvrPtoB-BAK1 complex reveals two structurally similar kinaseinteracting domains in a single type III effector
Components
  • BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
  • Effector protein HopAB2
KeywordsTRANSFERASE/LIGASE / Plant immunity / Pseudomonas syringae / Solanum lycopersicum / PAMP-triggered immunity / Bacterial pathogenesis / TRANSFERASE-LIGASE complex
Function / homology
Function and homology information


effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host programmed cell death / receptor serine/threonine kinase binding / Transferases; Acyltransferases; Aminoacyltransferases / transmembrane receptor protein tyrosine kinase activity / defense response / receptor protein-tyrosine kinase / transferase activity / non-specific serine/threonine protein kinase / endosome membrane ...effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host programmed cell death / receptor serine/threonine kinase binding / Transferases; Acyltransferases; Aminoacyltransferases / transmembrane receptor protein tyrosine kinase activity / defense response / receptor protein-tyrosine kinase / transferase activity / non-specific serine/threonine protein kinase / endosome membrane / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Effector protein HopAB, BAK1-interacting domain / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain ...Effector protein HopAB, BAK1-interacting domain / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Monooxygenase / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Effector protein HopAB2 / BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Pseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChai, J. / Cheng, W. / Gao, H.
CitationJournal: Cell Host Microbe / Year: 2011
Title: Structural Analysis of Pseudomonas syringae AvrPtoB Bound to Host BAK1 Reveals Two Similar Kinase-Interacting Domains in a Type III Effector.
Authors: Cheng, W. / Munkvold, K.R. / Gao, H. / Mathieu, J. / Schwizer, S. / Wang, S. / Yan, Y.B. / Wang, J. / Martin, G.B. / Chai, J.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
B: Effector protein HopAB2
D: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
F: Effector protein HopAB2
G: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
H: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
K: Effector protein HopAB2
L: Effector protein HopAB2


Theoretical massNumber of molelcules
Total (without water)212,5768
Polymers212,5768
Non-polymers00
Water3,387188
1
A: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
B: Effector protein HopAB2


Theoretical massNumber of molelcules
Total (without water)53,1442
Polymers53,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-11 kcal/mol
Surface area18400 Å2
MethodPISA
2
D: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
F: Effector protein HopAB2


Theoretical massNumber of molelcules
Total (without water)53,1442
Polymers53,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-11 kcal/mol
Surface area18640 Å2
MethodPISA
3
G: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
K: Effector protein HopAB2


Theoretical massNumber of molelcules
Total (without water)53,1442
Polymers53,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-14 kcal/mol
Surface area18780 Å2
MethodPISA
4
H: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
L: Effector protein HopAB2


Theoretical massNumber of molelcules
Total (without water)53,1442
Polymers53,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-12 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.836, 108.140, 83.247
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor ...AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor kinase 3 / AtSERK3 / Somatic embryogenesis receptor-like kinase 3


Mass: 40353.559 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 248-590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Production host: Escherichia coli (E. coli)
References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein
Effector protein HopAB2 / Avirulence protein AvrPtoB / E3 ubiquitin-protein ligase


Mass: 12790.556 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 250-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: hopAB2, avrPtoB, PSPTO_3087 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RSY1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLEAVED OF PRESCISSION PROTEASE CUT SITE

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.6M NH4Ac, PEG 3350 (v/v), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 5, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 65585 / Num. obs: 63725 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→55 Å / % possible all: 87.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QKW

2qkw


Resolution: 2.5→24.141 Å / SU ML: 0.43 / σ(F): 1.56 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 3247 5.1 %RANDOM
Rwork0.1836 ---
obs0.1864 56550 97.4 %-
all-65540 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.661 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6786 Å2-0 Å24.7561 Å2
2--6.6243 Å20 Å2
3----8.3028 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12456 0 0 188 12644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612645
X-RAY DIFFRACTIONf_angle_d1.0617077
X-RAY DIFFRACTIONf_dihedral_angle_d20.6198127
X-RAY DIFFRACTIONf_chiral_restr0.0691910
X-RAY DIFFRACTIONf_plane_restr0.0032225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.53730.34451210.2807238888
2.5373-2.57690.33621300.2861249292
2.5769-2.61910.37831420.29251994
2.6191-2.66420.32631300.2634257896
2.6642-2.71260.35511450.2615259297
2.7126-2.76470.29621440.2304263898
2.7647-2.82110.28071410.2144265498
2.8211-2.88230.30611490.2226264299
2.8823-2.94920.29681470.2211263699
2.9492-3.02290.3121500.2173266799
3.0229-3.10440.2981280.21266699
3.1044-3.19560.25341490.1943265599
3.1956-3.29850.28121250.1947269199
3.2985-3.41610.24081400.1942268299
3.4161-3.55240.24771560.1897264299
3.5524-3.71360.23591410.1777268899
3.7136-3.90860.22111470.1674267099
3.9086-4.15230.22321580.1588268099
4.1523-4.4710.18361260.1414269699
4.471-4.91760.18091600.145268999
4.9176-5.62130.24051340.1629270199
5.6213-7.05280.22861370.19112731100
7.0528-24.14260.17171470.1554248190
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)
10.2486-0.08760.02010.26990.0920.2408-0.07370.02370.0955-0.26020.1094-0.02310.1356-0.14970.03640.2883-0.1089-0.01050.18460.03920.13268.8336-4.724619.9695
20.1282-0.0477-0.01960.0478-0.03160.16450.14650.13470.3857-0.0137-0.08210.1077-0.4112-0.0068-0.01130.49950.03060.04270.21070.05770.54989.752619.137717.936
30.620.0098-0.24610.27050.03840.1070.05130.5382-0.0249-0.3833-0.2462-0.2707-0.0852-0.03210.0690.51170.07970.15130.60720.10050.372328.60521.1813.7529
40.1045-0.013-0.17480.0653-0.09370.4821-0.17170.4256-0.1369-0.03450.0544-0.0273-0.0681-0.1474-0.00970.214-0.0550.00940.7308-0.0430.241879.3927-7.4211-8.9155
50.7012-0.1558-0.4370.2573-0.22290.7275-0.11170.1034-0.38660.1435-0.03960.0683-0.0571-0.21040.06420.1737-0.02440.03330.22780.01920.2283-4.3493-10.438369.4358
60.07570.0373-0.0680.0740.00930.103-0.2536-0.2132-0.2719-0.0535-0.02710.04590.32340.6083-0.20610.04040.4718-0.09430.2830.17320.135164.4867-13.15339.9528
70.2976-0.0942-0.07660.1463-0.05420.2548-0.0918-0.62550.188-0.07140.1556-0.0647-0.44830.4283-0.02830.5248-0.0165-0.06250.6554-0.12540.284268.00969.258148.7248
80.60180.159-0.06560.1744-0.03810.4506-0.19130.23710.0514-0.1070.10210.0134-0.08560.10590.02440.187-0.00310.00270.21470.00970.148759.6804-6.40948.8698
90.45590.2855-0.14410.2727-0.2760.63720.13580.18120.57250.13640.03820.1506-0.42310.1466-0.05910.6071-0.1338-0.02070.40590.12060.539269.829315.68887.577
100.6108-0.1723-0.20720.0630.05120.1599-0.1008-0.2862-0.20430.0302-0.1170.08080.11-0.1746-0.01860.1440.1337-0.00930.72710.03780.249145.7853-8.161357.8288
110.3763-0.087-0.24650.19310.00350.3095-0.0109-0.27360.0054-0.0030.0236-0.1233-0.01980.0888-0.01670.1422-0.01470.01560.2095-0.02040.223814.5253-8.104151.5012
120.11960.074-0.01050.2553-0.11160.25470.2556-0.16180.5014-0.05950.1164-0.1044-0.27160.11480.18470.35760.0030.07670.2203-0.24540.50647.877914.321959.5989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 273:487
2X-RAY DIFFRACTION2chain A and resi 488:576
3X-RAY DIFFRACTION3chain B
4X-RAY DIFFRACTION4chain L
5X-RAY DIFFRACTION5chain F
6X-RAY DIFFRACTION6chain G and resi 274:487
7X-RAY DIFFRACTION7chain G and resi 488:578
8X-RAY DIFFRACTION8chain H and resi 274:487
9X-RAY DIFFRACTION9chain H and resi 488:578
10X-RAY DIFFRACTION10chain K
11X-RAY DIFFRACTION11chain D and resi 274:487
12X-RAY DIFFRACTION12chain D and resi 488:583

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