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- PDB-8xgl: Structure of the Magnaporthe oryzae effector NIS1 -

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Basic information

Entry
Database: PDB / ID: 8xgl
TitleStructure of the Magnaporthe oryzae effector NIS1
ComponentsNecrosis-inducing secreted protein 1
KeywordsPROTEIN BINDING / fungi / Magnaporthe oryzae / effector
Function / homologyNis1-like / Nis1 family / host cell cytoplasm / extracellular region / Necrosis-inducing secreted protein 1
Function and homology information
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHan, R. / Wang, D. / Zhang, X. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Understanding and manipulating the recognition of necrosis-inducing secreted protein 1 (NIS1) by BRI1-associated receptor kinase 1 (BAK1).
Authors: Han, R. / Zhu, T. / Kong, Z. / Zhang, X. / Wang, D. / Liu, J.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Necrosis-inducing secreted protein 1
B: Necrosis-inducing secreted protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5978
Polymers27,5242
Non-polymers1,0736
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-12 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.800, 129.800, 79.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Necrosis-inducing secreted protein 1 / Secreted effector NIS1


Mass: 13762.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: NIS1, MGG_02347 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G4MQL4
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.43 Å3/Da / Density % sol: 72.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-Tris (pH 6.5), 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→29.12 Å / Num. obs: 22307 / % possible obs: 99.86 % / Redundancy: 8.3 % / CC1/2: 0.992 / Net I/σ(I): 11.42
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 2237 / CC1/2: 0.594

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.3→29.12 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 1043 4.68 %
Rwork0.1775 --
obs0.1782 22301 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 67 91 1959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.702
X-RAY DIFFRACTIONf_dihedral_angle_d6.271287
X-RAY DIFFRACTIONf_chiral_restr0.079304
X-RAY DIFFRACTIONf_plane_restr0.006341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.25151900.25013042X-RAY DIFFRACTION100
2.42-2.570.22721940.21472964X-RAY DIFFRACTION100
2.57-2.770.25031080.21123084X-RAY DIFFRACTION100
2.77-3.050.23321400.21013036X-RAY DIFFRACTION100
3.05-3.490.21341550.18823023X-RAY DIFFRACTION100
3.49-4.390.15651480.153035X-RAY DIFFRACTION100
4.4-29.120.16821080.15643074X-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)
17.6519-7.4029-1.25329.4590.4754.84340.11-0.16170.17880.0348-0.1201-0.1624-0.11550.33220.17880.3823-0.04440.01580.46960.06470.4561-1.251129.4791-1.7901
29.9224-1.0024-0.38385.75720.17022.8242-0.19711.19410.50850.16860.0094-0.5484-1.05230.14090.2520.59450.0406-0.02350.34120.07040.405-15.171949.753-3.1603
34.4848-4.9973.15296.5084-3.67623.5640.07710.25980.07770.0398-0.4595-0.3767-0.13130.62550.50040.361-0.0260.01220.46770.05570.456-1.374631.0524-2.7041
44.6985-1.00610.85525.412-0.94823.47170.0105-0.24950.11040.21580.003-0.2811-0.55250.0283-0.03490.3951-0.0271-0.02450.38150.00580.4105-12.64935.53017.1665
52.693.2344-4.54864.6365-5.52468.2678-0.3456-0.0399-0.4909-0.875-0.2961-1.07441.21731.060.64570.54280.11540.06840.58190.03290.724-5.127427.3771-8.0193
67.5814-2.386-2.03696.86181.09225.8083-0.4136-0.37570.1720.59120.14380.2526-0.2231-0.44720.12450.53520.0588-0.03630.36080.01870.377-16.611943.8036-1.6918
72.7401-2.1372-0.09487.72480.71753.3120.038-0.03020.13010.2112-0.1581-0.4166-0.42350.14410.07320.3532-0.0498-0.04460.3436-0.00870.3581-8.844236.60835.7566
83.012-5.3749-2.08379.07664.41973.3752-0.00040.0668-0.4366-0.6387-0.27780.7016-0.0064-0.09550.27520.4237-0.063-0.03270.3795-0.03330.5317-22.191912.57475.4359
91.355-1.7405-0.94425.72281.20391.1880.11330.1249-0.066-0.3236-0.1894-0.0743-0.1344-0.24930.12330.35250.011-0.02130.3729-0.02750.3895-21.935719.4117.2847
100.8591-1.88860.6897.3545-1.02535.48070.1766-0.3742-0.22811.09910.6565-0.23320.5520.5663-0.73650.74510.0339-0.10530.5251-0.02290.5528-6.229212.841215.0071
119.5761-5.39452.76919.4963-2.10346.52830.05780.3475-0.5913-0.776-0.2427-0.62690.32410.11210.11740.40570.00320.05080.3521-0.02920.3987-12.680715.9335-0.4423
128.39441.7898-3.81645.4832.25555.6681-0.24320.56840.2527-0.65680.23420.28230.0009-1.1646-0.09450.52170.121-0.16770.5711-0.0080.5305-26.232923.9379-1.0563
133.1048-1.8701-0.8458.04721.68341.3306-0.0535-0.0596-0.36220.0763-0.0504-0.01270.1131-0.02220.08030.3844-0.00310.03360.32940.01660.3718-16.030813.67365.0819
142.81250.8416-0.04312.72490.91792.2327-0.0513-0.061-0.40730.8654-0.04870.53130.37780.02430.00520.3913-0.02330.00950.39320.05910.4431-15.031611.6749.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 105 )
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 137 )
8X-RAY DIFFRACTION8chain 'B' and (resid -3 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 57 )
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 137 )

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