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- PDB-9imu: The complex of rice immune receptor RGA5-HMA8 with rice blast eff... -

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Basic information

Entry
Database: PDB / ID: 9imu
TitleThe complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR-PikD
Components
  • AVR-Pik protein
  • Disease resistance protein RGA5
KeywordsPLANT PROTEIN / NLR receptor / HMA domain / Non-MAX effector / Rice / Resistance
Function / homology
Function and homology information


innate immune response-activating signaling pathway / plant-type hypersensitive response / ADP binding / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. ...: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix 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 / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AVR-Pik protein / Disease resistance protein RGA5
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZhang, X. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The complex of rice immune receptor RGA5-HMA8 with rice blast effector protein AVR-PikD
Authors: Zhang, X. / Liu, J.
History
DepositionJul 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 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: Disease resistance protein RGA5
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers17,4802
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-5 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.410, 66.410, 84.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Disease resistance protein RGA5 / Os11gRGA5 / SasRGA5 / HMA8 protein


Mass: 8077.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: RGA5 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J0N2
#2: Protein AVR-Pik protein / AvrPi7 protein


Mass: 9402.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 8536 / % possible obs: 99.8 % / Redundancy: 19.3 % / CC1/2: 0.986 / Net I/σ(I): 45.2
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 410 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 2.38→34.04 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 855 10.07 %
Rwork0.1957 --
obs0.1998 8493 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 21 1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091255
X-RAY DIFFRACTIONf_angle_d1.2991696
X-RAY DIFFRACTIONf_dihedral_angle_d28.738167
X-RAY DIFFRACTIONf_chiral_restr0.066185
X-RAY DIFFRACTIONf_plane_restr0.008219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.530.27891390.24541257X-RAY DIFFRACTION100
2.53-2.730.32411400.22671271X-RAY DIFFRACTION100
2.73-30.29171450.26191273X-RAY DIFFRACTION100
3-3.430.26361430.2211270X-RAY DIFFRACTION100
3.43-4.320.22951480.18271273X-RAY DIFFRACTION100
4.32-34.040.19921400.16581294X-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)
11.96140.5318-0.37354.2522-0.47344.4253-0.0431.05070.7442-0.44820.1555-1.3207-0.3341-0.0233-0.00660.4332-0.05160.14910.4693-0.00190.70426.311-3.5851-10.5474
25.2903-2.0228-1.74534.1203-2.44384.2078-0.111-0.8513-1.1991-0.5410.5373-1.1717-0.54720.9018-0.28860.7449-0.06850.18640.80930.10011.107731.47042.3652-16.616
33.62470.168-2.95726.3876-0.73164.6867-0.08680.03780.86430.1926-0.0018-1.0638-0.81380.49550.1730.6852-0.0191-0.06220.4494-0.03020.732124.8645-0.2761-9.2895
47.70220.2124-2.71044.9397-0.31865.2379-0.12683.0237-0.2805-1.7488-0.2262-0.66080.07160.46880.17960.7357-0.0340.08550.6505-0.06060.462723.1008-6.1301-19.6863
53.38270.09190.79012.9487-0.52935.9220.15430.04560.4679-0.2123-0.2473-1.00580.0820.34120.21770.39750.03510.03620.41310.08760.608721.3439-8.0204-7.0851
62.3232-1.7046-0.65168.8337-0.3954.07460.85560.1625-0.4449-0.1573-0.9477-1.05930.25890.60010.09450.65790.0612-0.11940.8976-0.05110.728831.3286-6.18646.5765
73.6921-0.6733-1.53455.26030.27734.38450.2313-0.1714-0.56650.6254-0.3117-0.95890.25960.1479-0.00210.51130.0044-0.12240.38250.01350.517225.8905-10.22514.485
86.2142-0.1469-0.2155.9824-0.83682.58850.09-0.4587-0.26750.49750.0324-0.33190.2430.0565-0.08390.45940.0269-0.0750.41390.06130.374621.7336-13.90643.3666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 996 through 1009 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1010 through 1020 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1021 through 1046 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1047 through 1058 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1059 through 1070 )
6X-RAY DIFFRACTION6chain 'C' and (resid 33 through 47 )
7X-RAY DIFFRACTION7chain 'C' and (resid 48 through 62 )
8X-RAY DIFFRACTION8chain 'C' and (resid 63 through 113 )

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