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- PDB-5zng: The crystal complex of immune receptor RGA5A_S of Pia from rice (... -

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Basic information

Entry
Database: PDB / ID: 5zng
TitleThe crystal complex of immune receptor RGA5A_S of Pia from rice (Oryzae sativa) with rice blast (Magnaporthe oryzae) effector protein AVR1-CO39
Components
  • AVR1-CO39
  • NBS-LRR type protein
KeywordsIMMUNE SYSTEM / RGA5A_S / resistance protein / rice AVR1-CO39 / effector protein / Magnaporthe oryzae
Function / homology
Function and homology information


plant-type hypersensitive response / innate immune response-activating signaling pathway / ADP binding / : / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat domain superfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein RGA5 / Uncharacterized protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å
AuthorsGuo, L.W. / Zhang, Y.K. / Liu, Q. / Ma, M.Q. / Liu, J.F. / Peng, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China315711057 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces
Authors: Guo, L. / Cesari, S. / de Guillen, K. / Chalvon, V. / Mammri, L. / Ma, M. / Meusnier, I. / Bonnot, F. / Padilla, A. / Peng, Y.L. / Liu, J. / Kroj, T.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NBS-LRR type protein
C: AVR1-CO39


Theoretical massNumber of molelcules
Total (without water)24,0042
Polymers24,0042
Non-polymers00
Water66737
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)66.721, 66.721, 108.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NBS-LRR type protein


Mass: 14895.397 Da / Num. of mol.: 1 / Fragment: S domain
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os11gRGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2
#2: Protein AVR1-CO39


Mass: 9108.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8J180
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.1 M ammonium tartrate dibasic 0.1 M sodium acetate-HCl, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.108→39.47 Å / Num. obs: 215689 / % possible obs: 1 % / Redundancy: 13.1 % / Net I/σ(I): 10.11
Reflection shellResolution: 2.189→2.268 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MYV

2myv


Resolution: 2.189→28.405 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.57 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.1966 1262 4.7 %
Rwork0.1619 --
obs0.1635 26844 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.189→28.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 0 37 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081101
X-RAY DIFFRACTIONf_angle_d0.8861490
X-RAY DIFFRACTIONf_dihedral_angle_d10.265676
X-RAY DIFFRACTIONf_chiral_restr0.066177
X-RAY DIFFRACTIONf_plane_restr0.005190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1895-2.27710.2787820.26612417X-RAY DIFFRACTION81
2.2771-2.38070.26321630.22292675X-RAY DIFFRACTION91
2.3807-2.50610.25391580.22092847X-RAY DIFFRACTION98
2.5061-2.6630.29141340.2162973X-RAY DIFFRACTION100
2.663-2.86850.25361770.2072902X-RAY DIFFRACTION100
2.8685-3.15680.23291360.19062951X-RAY DIFFRACTION100
3.1568-3.61280.20621270.16882958X-RAY DIFFRACTION100
3.6128-4.54880.17541690.13212922X-RAY DIFFRACTION100
4.5488-28.40740.13361160.13072937X-RAY DIFFRACTION99
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)
11.4768-1.9491-1.61915.04323.34232.6436-0.6683-3.5838-0.80991.04491.1526-1.95231.1274-0.176-1.54350.80010.23090.06861.36630.35071.0526-10.918720.5728-14.6554
24.2429-1.45344.19567.7581-1.26587.6491-0.0298-1.46580.3199-0.236-0.1405-0.0405-0.1111-0.98150.1340.2929-0.06940.02750.7634-0.04590.4583-22.477329.4918-26.5139
38.5286-4.58853.11443.8146-3.04262.4834-0.1245-0.3444-0.0944-0.290.38740.70010.2306-0.7049-0.17780.3223-0.0209-0.03210.62850.02650.5569-31.089824.846-26.9763
45.9415-0.2918-0.72527.729-3.01438.7148-0.2781-0.6714-0.04850.42970.10790.0509-0.17720.48860.34090.26710.0410.04440.764-0.06460.425-24.771726.4537-19.0506
56.5499-2.07531.75043.2726-0.51435.6698-0.1723-0.8060.5750.02930.0178-0.0735-0.31670.61940.38010.3670.02050.02810.6384-0.05540.4831-22.082230.3241-23.4997
65.1781-2.51124.55326.3651-2.38633.97080.3102-0.3337-0.5962-0.8702-0.0072-0.2541.17330.1836-0.09120.50360.00030.0550.60430.0110.4926-21.188419.5114-29.7016
79.42133.77285.75879.66552.59593.7526-0.0061-1.26360.1091-0.1805-0.1012-0.1972-0.29660.4505-0.03340.2489-0.07190.01980.8423-0.0690.5228-15.584129.4454-25.4719
85.85981.0224-1.05712.8684-2.07017.6944-0.12970.50530.1196-0.259-0.11860.2220.01110.01420.14330.33240.00310.03970.7706-0.04730.4877-33.261127.4726-17.0053
95.6154-0.7711.38012.1265-1.55776.856-0.0082-0.21120.15620.6268-0.4786-1.1423-0.27470.57370.48230.30140.03850.00220.64840.0180.5511-32.254426.626-5.9338
105.5752-0.8923-1.16348.6848-0.20354.4434-0.33260.236-0.051-0.00790.18850.3077-0.0169-0.24110.14350.26280.06220.01220.6768-0.06570.4478-39.889428.0274-10.363
112.24431.02060.64120.49380.20020.48380.55612.1131-1.1773-1.04911.2274-1.26092.37880.2907-2.10921.1220.04110.15681.0454-0.37470.9554-35.171112.2692-18.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 991 through 996 )
2X-RAY DIFFRACTION2chain 'A' and (resid 997 through 1008 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1009 through 1021 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1022 through 1031 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1032 through 1046 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1047 through 1058 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1059 through 1069 )
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 42 )
9X-RAY DIFFRACTION9chain 'C' and (resid 43 through 57 )
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 78 )
11X-RAY DIFFRACTION11chain 'C' and (resid 79 through 83 )

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