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- PDB-6g11: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 6g11
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with the HMA domain of Pikp-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • Resistance protein Pikp-1
KeywordsANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype ...AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AVR-Pik protein / Resistance protein Pikp-1
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
Oryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDe la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J00453 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012574 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M02198X United Kingdom
European Research Council743165
Japan Society for the Promotion of ScienceKAKENHI 15H05779 Japan
CitationJournal: Nat Plants / Year: 2018
Title: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
Authors: De la Concepcion, J.C. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: AVR-Pik protein
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1
F: AVR-Pik protein
D: Resistance protein Pikp-1
E: Resistance protein Pikp-1


Theoretical massNumber of molelcules
Total (without water)55,1026
Polymers55,1026
Non-polymers00
Water4,089227
1
C: AVR-Pik protein
A: Resistance protein Pikp-1
B: Resistance protein Pikp-1


Theoretical massNumber of molelcules
Total (without water)27,5513
Polymers27,5513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: AVR-Pik protein
D: Resistance protein Pikp-1
E: Resistance protein Pikp-1


Theoretical massNumber of molelcules
Total (without water)27,5513
Polymers27,5513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.196, 80.177, 105.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21F
12A
22B
13A
23D
14A
24E
15B
25D
16B
26E
17D
27E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label alt-ID
11ALAALAPHEPHECA32 - 11312 - 93
21ALAALAPHEPHEFD32 - 11312 - 93
12LYSLYSGLNGLNAB188 - 2595 - 76
22LYSLYSGLNGLNBC188 - 2595 - 76
13LYSLYSALAALAAB188 - 2605 - 77
23LYSLYSALAALADE188 - 2605 - 77
14LYSLYSGLNGLNAB188 - 2595 - 76
24LYSLYSGLNGLNEF188 - 2595 - 76A
15LYSLYSGLNGLNBC188 - 2595 - 76
25LYSLYSGLNGLNDE188 - 2595 - 76
16LYSLYSASPASPBC188 - 2635 - 80A
26LYSLYSASPASPEF188 - 2635 - 80A
17LYSLYSGLNGLNDE188 - 2595 - 76
27LYSLYSGLNGLNEF188 - 2595 - 76A

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein AVR-Pik protein


Mass: 10803.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: C4B8C2
#2: Protein
Resistance protein Pikp-1


Mass: 8373.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pikp-1 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: E9KPB5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 1 (1M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 4 (25%v/v ...Details: 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 1 (1M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→46.29 Å / Num. obs: 45720 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.94 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.5.328data reduction
Aimless0.5.32data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 1.9→46.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.276 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22443 2178 4.8 %RANDOM
Rwork0.20876 ---
obs0.20954 43475 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.046 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å20 Å20 Å2
2--4.84 Å20 Å2
3----1.88 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 227 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193535
X-RAY DIFFRACTIONr_bond_other_d0.0020.023507
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9754761
X-RAY DIFFRACTIONr_angle_other_deg0.89338140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23624.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8891520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9343.3291816
X-RAY DIFFRACTIONr_mcbond_other2.9313.3271815
X-RAY DIFFRACTIONr_mcangle_it4.2254.9492254
X-RAY DIFFRACTIONr_mcangle_other4.2254.9512255
X-RAY DIFFRACTIONr_scbond_it3.7133.7881719
X-RAY DIFFRACTIONr_scbond_other3.7073.7841717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6675.4612504
X-RAY DIFFRACTIONr_long_range_B_refined7.75839.0153802
X-RAY DIFFRACTIONr_long_range_B_other7.72338.863762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C52020.06
12F52020.06
21A36320.13
22B36320.13
31A38660.07
32D38660.07
41A36100.13
42E36100.13
51B37080.12
52D37080.12
61B41420.06
62E41420.06
71D36340.13
72E36340.13
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 166 -
Rwork0.319 3145 -
obs--99.7 %

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