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- PDB-5zne: The crystal structure of immune receptor RGA5A_S of resistance pr... -

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Basic information

Entry
Database: PDB / ID: 5zne
TitleThe crystal structure of immune receptor RGA5A_S of resistance protein Pia from rice (Oryza sativa)
ComponentsNBS-LRR type protein
KeywordsPLANT PROTEIN / RGA5A_S / Resistance Protein / Rice
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
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGuo, L.W. / Huang, D. / Liu, J.F. / Peng, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)3157110057 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 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NBS-LRR type protein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water73941
1
A: NBS-LRR type protein

A: NBS-LRR type protein


Theoretical massNumber of molelcules
Total (without water)29,7912
Polymers29,7912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)55.619, 55.619, 78.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1231-

HOH

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Components

#1: Protein NBS-LRR type protein / RGA5A


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.18 M ammonium nitrate 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→55.08 Å / Num. obs: 21743 / % possible obs: 99.84 % / Redundancy: 2 % / Net I/σ(I): 20.05
Reflection shellResolution: 2.234→2.314 Å / Redundancy: 2 % / Rmerge(I) obs: 0.01194 / Num. unique obs: 6259 / CC1/2: 1 / Rrim(I) all: 0.01688 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DXS

3dxs


Resolution: 1.78→45.35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 27.88
RfactorNum. reflection% reflection
Rfree0.2376 616 5.16 %
Rwork0.2179 --
obs0.2189 21743 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms543 0 0 41 584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006557
X-RAY DIFFRACTIONf_angle_d0.805751
X-RAY DIFFRACTIONf_dihedral_angle_d8.439488
X-RAY DIFFRACTIONf_chiral_restr0.06296
X-RAY DIFFRACTIONf_plane_restr0.00594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.8610.32861540.31962638X-RAY DIFFRACTION99
1.861-1.95920.45571190.39552295X-RAY DIFFRACTION86
1.9592-2.08190.26371500.24352621X-RAY DIFFRACTION99
2.0819-2.24270.26161460.23212498X-RAY DIFFRACTION94
2.2427-2.46830.22141310.25062550X-RAY DIFFRACTION95
2.4683-2.82550.25241450.22812677X-RAY DIFFRACTION100
2.8255-3.55960.20161380.20742668X-RAY DIFFRACTION100
3.5596-45.36520.22241400.18562673X-RAY DIFFRACTION100
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)
19.1133.20130.4877.0162-0.93947.62840.2527-0.4529-0.02770.0413-0.4977-0.1449-0.02390.7640.26320.1658-0.0255-0.02790.2740.00620.1882-4.14522.543-9.8199
22.738-1.0964-7.79275.92870.89172.6991-0.01520.35330.3971-0.2145-0.0419-0.2096-0.51250.32370.14390.3137-0.0671-0.11390.41330.06020.29071.637229.2751-6.5332
33.0216-0.2359-2.96187.69810.57217.58020.226-0.4292-0.2283-0.0707-0.38580.3421-0.132-0.07130.22010.27550.0026-0.01230.3114-0.00810.2065-4.505622.603-0.3459
44.0817-0.4155-1.22049.8509-1.171910.25070.20340.2069-0.3672-0.274-0.3704-0.03680.6262-0.3030.11740.2529-0.0088-0.06550.3144-0.0470.1995-4.834820.1408-7.424
52.67096.0641-1.11533.1058-3.69992.9028-0.3395-0.11561.58770.307-0.00920.7328-1.6358-0.69980.33110.57580.1094-0.07640.4998-0.00680.5589-9.810530.9175-9.5898
610.81626.3051-7.00313.5709-5.25528.7621-0.2292-0.1585-0.47650.003-0.2743-0.510.5245-0.38030.54690.3285-0.0771-0.01990.33290.00430.2647-10.825919.4457-10.6352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 997 through 1008 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1009 through 1020 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1021 through 1031 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1032 through 1046 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1047 through 1058 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1059 through 1069 )

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