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- PDB-6qup: Structural signatures in EPR3 define a unique class of plant carb... -

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Basic information

Entry
Database: PDB / ID: 6qup
TitleStructural signatures in EPR3 define a unique class of plant carbohydrate receptors
Components
  • LysM type receptor kinase
  • Nanobody 186 (Nb186)
KeywordsPLANT PROTEIN / LysM Protein / Nitrogen Fixation / Plant Receptor
Function / homology
Function and homology information


membrane => GO:0016020 / protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain superfamily / LysM domain profile. / LysM domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...LysM domain superfamily / LysM domain profile. / LysM domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.871 Å
AuthorsWong, J.E. / Gysel, K. / Birkefeldt, T.G. / Vinther, M. / Muszynski, A. / Azadi, P. / Laursen, N.S. / Sullivan, J.T. / Ronson, C.W. / Stougaard, J. / Andersen, K.R.
CitationJournal: Nat Commun / Year: 2020
Title: Structural signatures in EPR3 define a unique class of plant carbohydrate receptors.
Authors: Wong, J.E.M.M. / Gysel, K. / Birkefeldt, T.G. / Vinther, M. / Muszynski, A. / Azadi, P. / Laursen, N.S. / Sullivan, J.T. / Ronson, C.W. / Stougaard, J. / Andersen, K.R.
History
DepositionFeb 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Jan 24, 2024Group: 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: LysM type receptor kinase
B: Nanobody 186 (Nb186)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,93210
Polymers37,2822
Non-polymers6508
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint25 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.822, 36.083, 72.661
Angle α, β, γ (deg.)90.000, 93.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein LysM type receptor kinase


Mass: 23294.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KU53
#2: Antibody Nanobody 186 (Nb186)


Mass: 13987.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): LOBSTR / Production host: Escherichia coli BL21 (bacteria)
#3: 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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 3 types, 176 molecules

#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium Citrate pH 5.5, 20% PEG 4000, 18% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.87→72.491 Å / Num. obs: 25177 / % possible obs: 96.94 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.76 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.96
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 2151 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EBZ

4ebz


Resolution: 1.871→72.491 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 2000 7.95 %
Rwork0.1628 23173 -
obs0.1666 25173 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.04 Å2 / Biso mean: 45.2955 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: final / Resolution: 1.871→72.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 103 170 2615
Biso mean--92.7 44.53 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8711-1.91790.34241130.2857138582
1.9179-1.96970.28681480.243153693
1.9697-2.02770.23781300.1997168499
2.0277-2.09320.23641440.2031163998
2.0932-2.1680.2841420.1971168199
2.168-2.25480.22881520.1849171099
2.2548-2.35740.22111450.1742162698
2.3574-2.48170.24451410.1746169699
2.4817-2.63720.21851500.1644168399
2.6372-2.84080.2511400.1713170499
2.8408-3.12670.21421390.1648168899
3.1267-3.57910.19051530.1413167998
3.5791-4.50930.17791500.1317171799
4.5093-72.490.17851530.1544174598
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)
13.23710.12861.06442.60340.33753.8091-0.045-0.2640.0660.19410.04580.07750.0222-0.12440.020.30730.00550.00960.2001-0.02630.223359.55557.405124.4215
26.0707-0.8299-0.7381.18440.34952.7635-0.0112-0.2294-0.04670.06670.1155-0.09590.08660.1512-0.09910.31540.0232-0.00740.1917-0.00330.177761.273-0.377524.1877
34.2449-3.04055.89983.2202-5.058.91870.79410.8628-0.9998-0.5264-0.04640.05930.76520.6647-0.4960.42750.0009-0.03270.4068-0.13260.351748.5605-9.7241-0.6754
44.0301-1.3012-0.22741.88231.96292.42150.23650.2868-0.326-0.4227-0.13090.5906-0.0442-0.2278-0.01460.283-0.0288-0.01820.25510.01520.188536.87712.4479-4.4701
54.4896-0.81370.9735.9728-1.16714.09810.21990.0534-0.54510.2435-0.1154-0.13210.4264-0.0009-0.01370.3194-0.0149-0.01450.1933-0.02240.230547.4796-3.74675.8496
66.56544.4587-6.06465.2844-6.95249.6347-0.06530.14290.12990.1134-0.1599-0.3791-0.39510.33260.14960.3184-0.0364-0.00040.26980.03180.217648.92767.21572.6828
75.6534-1.14090.64646.7175-6.32248.66420.0669-0.28180.03690.42990.27820.0164-0.2825-0.45-0.36230.36340.00620.01950.24760.0060.188541.92741.722813.641
85.5121.060.83211.44851.61664.59320.2239-0.2967-0.25360.6312-0.2255-0.16560.1424-0.26330.01280.2904-0.03360.00860.27290.03580.1937.6081.24445.1102
93.8591-2.56440.1835.5645-3.72786.67110.14150.3490.5154-0.1559-0.4071-0.4388-0.21030.13930.34190.2355-0.0887-0.03980.209-0.01030.211843.79676.5943-0.6957
105.3473-5.59964.57967.9911-6.67265.98750.13680.48880.2152-0.188-0.2302-0.1713-0.00740.38190.01340.2671-0.03360.01860.2661-0.01120.25348.77550.443-0.2295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 116 )A36 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 217 )A117 - 217
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 8 )B1 - 8
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 27 )B9 - 27
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 40 )B28 - 40
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 53 )B41 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 60 )B54 - 60
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 83 )B61 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 99 )B84 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 119 )B100 - 119

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