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- PDB-8bv0: Binary complex between the NB-ARC domain from the Tomato immune r... -

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Basic information

Entry
Database: PDB / ID: 8bv0
TitleBinary complex between the NB-ARC domain from the Tomato immune receptor NRC1 and the SPRY domain-containing effector SS15 from the potato cyst nematode
Components
  • NRC1
  • Truncated secreted SPRY domain-containing protein 15 (Fragment)
KeywordsPROTEIN BINDING / NLR / inhibitor / effector / SPRYSEC / nematode
Function / homology
Function and homology information


defense response to other organism / ADP binding
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / SPRY domain / B30.2/SPRY domain ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Truncated secreted SPRY domain-containing protein 15 / NRC1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Globodera rostochiensis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsContreras, M.P. / Pai, H. / Muniyandi, S. / Toghani, A. / Lawson, D.M. / Tumtas, Y. / Duggan, C. / Yuen, E.L.H. / Stevenson, C.E.M. / Harant, A. ...Contreras, M.P. / Pai, H. / Muniyandi, S. / Toghani, A. / Lawson, D.M. / Tumtas, Y. / Duggan, C. / Yuen, E.L.H. / Stevenson, C.E.M. / Harant, A. / Wu, C.H. / Bozkurt, T.O. / Kamoun, S. / Derevnina, L.
Funding support United Kingdom, Germany, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDBoostR Germany
The Gatsby Charitable Foundation United Kingdom
CitationJournal: Sci Adv / Year: 2023
Title: Resurrection of plant disease resistance proteins via helper NLR bioengineering.
Authors: Contreras, M.P. / Pai, H. / Selvaraj, M. / Toghani, A. / Lawson, D.M. / Tumtas, Y. / Duggan, C. / Yuen, E.L.H. / Stevenson, C.E.M. / Harant, A. / Maqbool, A. / Wu, C.H. / Bozkurt, T.O. / ...Authors: Contreras, M.P. / Pai, H. / Selvaraj, M. / Toghani, A. / Lawson, D.M. / Tumtas, Y. / Duggan, C. / Yuen, E.L.H. / Stevenson, C.E.M. / Harant, A. / Maqbool, A. / Wu, C.H. / Bozkurt, T.O. / Kamoun, S. / Derevnina, L.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NRC1
B: Truncated secreted SPRY domain-containing protein 15 (Fragment)
C: NRC1
D: Truncated secreted SPRY domain-containing protein 15 (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1796
Polymers129,3254
Non-polymers8542
Water00
1
A: NRC1
B: Truncated secreted SPRY domain-containing protein 15 (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0903
Polymers64,6632
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NRC1
D: Truncated secreted SPRY domain-containing protein 15 (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0903
Polymers64,6632
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.560, 128.560, 170.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein NRC1


Mass: 40151.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallized protein sequence begins with a non-native GLY-PRO dipeptide left over from cleavage of N-terminal affinity tag.
Source: (gene. exp.) Solanum lycopersicum (tomato) / Plasmid: pOPIN-S3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / References: UniProt: A1X877
#2: Protein Truncated secreted SPRY domain-containing protein 15 (Fragment)


Mass: 24511.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallized protein sequence begins with a non-native GLY-PRO dipeptide left over from cleavage of N-terminal affinity tag.
Source: (gene. exp.) Globodera rostochiensis (invertebrata) / Plasmid: pOPIN-S3C / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: A0A024E1S8
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: NULL / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.5→51.34 Å / Num. obs: 8981 / % possible obs: 94 % / Redundancy: 8.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.026 / Rrim(I) all: 0.088 / Net I/σ(I): 7.2 / Num. measured all: 77102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.5-5.036.11.5131386522630.5880.6421.6511.584
10.06-51.3413.30.055115738710.9970.0160.05720.699.1

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Processing

Software
NameVersionClassification
Aimless0.7.8data scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→51.34 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU ML: 1.649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 883 9.9 %RANDOM
Rwork0.2374 ---
obs0.2409 8075 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 193.86 Å2 / Biso mean: 103.073 Å2 / Biso min: 58.48 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å22.01 Å20 Å2
2--4.01 Å2-0 Å2
3----13.02 Å2
Refinement stepCycle: final / Resolution: 4.5→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8796 0 54 0 8850
Biso mean--69.12 --
Num. residues----1096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0129056
X-RAY DIFFRACTIONr_bond_other_d0.0020.0168222
X-RAY DIFFRACTIONr_angle_refined_deg0.7941.6512266
X-RAY DIFFRACTIONr_angle_other_deg0.2991.56519182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11351092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.275562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.465101578
X-RAY DIFFRACTIONr_chiral_restr0.0370.21324
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021838
LS refinement shellResolution: 4.501→4.617 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 43 -
Rwork0.49 365 -
all-408 -
obs--57.55 %
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)
12.3908-0.8886-0.81014.6265-1.40152.36270.0728-0.0516-0.7764-0.7927-0.28240.22520.58230.76150.20960.42320.1492-0.12690.6353-0.05180.5211-47.901-26.13196.389
21.41080.0121-1.21450.5144-1.38517.5610.17440.3430.55720.2131-0.3339-0.5963-0.30621.35090.15950.7138-0.0993-0.13460.9210.20681.3098-27.94634.22735.2648
33.57121.14141.38874.2257-1.69532.3637-0.1862-0.14030.00650.1580.34260.9187-0.4703-0.1558-0.15640.57210.2024-0.08550.2427-0.00490.7907-54.9305-48.513731.0169
42.39741.8877-2.46283.0288-1.22354.80030.5684-1.1056-0.45050.5703-0.7331-0.32680.13470.11760.16470.8685-0.2011-0.15141.25580.54211.0631-38.594-73.74851.0782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 494
2X-RAY DIFFRACTION2B18 - 223
3X-RAY DIFFRACTION3C153 - 494
4X-RAY DIFFRACTION4D18 - 223

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