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- PDB-6s6q: Crystal structure of the LRR ectodomain of the plant membrane rec... -

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Basic information

Entry
Database: PDB / ID: 6s6q
TitleCrystal structure of the LRR ectodomain of the plant membrane receptor kinase GASSHO1/SCHENGEN3 from Arabidopsis thaliana in complex with CASPARIAN STRIP INTEGRITY FACTOR 2.
Components
  • LRR receptor-like serine/threonine-protein kinase GSO1
  • Protein CASPARIAN STRIP INTEGRITY FACTOR 2
KeywordsSIGNALING PROTEIN / membrane receptor kinase / leucine-rich repeat domain / peptide hormone identification / Casparian strip / root development / receptor activation
Function / homology
Function and homology information


specification of plant organ axis polarity / regulation of endodermal cell differentiation / : / Casparian strip / regulation of root morphogenesis / regulation of root development / pollen tube growth / protein serine/threonine kinase activity => GO:0004674 / monoatomic ion homeostasis / : ...specification of plant organ axis polarity / regulation of endodermal cell differentiation / : / Casparian strip / regulation of root morphogenesis / regulation of root development / pollen tube growth / protein serine/threonine kinase activity => GO:0004674 / monoatomic ion homeostasis / : / water transport / multicellular organism development / regulation of cell fate specification / potassium ion homeostasis / response to acidic pH / response to iron ion / regulation of cell division / endodermal cell differentiation / establishment of protein localization / hormone activity / cell wall organization / response to wounding / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Protein Casparian strip integrity factor 1/2 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site ...Protein Casparian strip integrity factor 1/2 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
LRR receptor-like serine/threonine-protein kinase GSO1 / Protein CASPARIAN STRIP INTEGRITY FACTOR 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsOkuda, S. / Moretti, A. / Hothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_176237 Switzerland
Swiss National Science Foundation31CP30_180213 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular mechanism for the recognition of sequence-divergent CIF peptides by the plant receptor kinases GSO1/SGN3 and GSO2.
Authors: Okuda, S. / Fujita, S. / Moretti, A. / Hohmann, U. / Doblas, V.G. / Ma, Y. / Pfister, A. / Brandt, B. / Geldner, N. / Hothorn, M.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: LRR receptor-like serine/threonine-protein kinase GSO1
B: LRR receptor-like serine/threonine-protein kinase GSO1
C: Protein CASPARIAN STRIP INTEGRITY FACTOR 2
D: Protein CASPARIAN STRIP INTEGRITY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,98531
Polymers193,3074
Non-polymers7,67827
Water00
1
A: LRR receptor-like serine/threonine-protein kinase GSO1
C: Protein CASPARIAN STRIP INTEGRITY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,58117
Polymers96,6532
Non-polymers3,92815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint47 kcal/mol
Surface area35520 Å2
MethodPISA
2
B: LRR receptor-like serine/threonine-protein kinase GSO1
D: Protein CASPARIAN STRIP INTEGRITY FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,40414
Polymers96,6532
Non-polymers3,75012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint41 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.360, 192.360, 149.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein LRR receptor-like serine/threonine-protein kinase GSO1 / Protein GASSHO 1 / Protein SCHENGEN 3


Mass: 94177.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: root / Gene: GSO1, SGN3, At4g20140, F1C12.60 / Plasmid: pBB2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Ao38
References: UniProt: C0LGQ5, non-specific serine/threonine protein kinase
#2: Protein/peptide Protein CASPARIAN STRIP INTEGRITY FACTOR 2


Mass: 2475.882 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: O65684

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Sugars , 4 types, 27 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 20
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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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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17 % [w/v] PEG 6,000, 0.1 M Tris pH 7.5, 0.2 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000006 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000006 Å / Relative weight: 1
ReflectionResolution: 2.95→48.3 Å / Num. obs: 59526 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 41 % / CC1/2: 1 / Rrim(I) all: 0.237 / Rsym value: 0.234 / Net I/σ(I): 19.1
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 40 % / Num. unique obs: 4336 / CC1/2: 0.48 / Rrim(I) all: 4.54 / Rsym value: 4.49 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GR8

5gr8


Resolution: 2.95→48.3 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2797 2962 4.98 %
Rwork0.209 --
obs0.2124 54498 99.94 %
Displacement parametersBiso mean: 103.56 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13080 0 495 0 13575

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