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- PDB-7odv: Plant peptide hormone receptor complex H1LS1 -

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Basic information

Entry
Database: PDB / ID: 7odv
TitlePlant peptide hormone receptor complex H1LS1
Components
  • Protein IDA
  • Receptor-like protein kinase HSL1
  • Somatic embryogenesis receptor kinase 1
KeywordsPEPTIDE BINDING PROTEIN / Plant receptor LRR pepide hormone / PEPTIDE BINDING PROTEIN Complex
Function / homology
Function and homology information


lateral root morphogenesis / regulation of cell diameter / microsporogenesis / floral organ abscission / pollen maturation / leaf abscission / response to ethylene / brassinosteroid mediated signaling pathway / pectin catabolic process / embryo development ending in seed dormancy ...lateral root morphogenesis / regulation of cell diameter / microsporogenesis / floral organ abscission / pollen maturation / leaf abscission / response to ethylene / brassinosteroid mediated signaling pathway / pectin catabolic process / embryo development ending in seed dormancy / apoplast / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / regulation of gene expression / defense response to Gram-negative bacterium / protein phosphorylation / non-specific serine/threonine protein kinase / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Protein IDA-like / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase ...Protein IDA-like / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Protein IDA / Somatic embryogenesis receptor kinase 1 / Receptor-like protein kinase HSL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsRoman, A.O. / Jimenez-Sandoval, P. / Santiago, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_173101 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: HSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides.
Authors: Roman, A.O. / Jimenez-Sandoval, P. / Augustin, S. / Broyart, C. / Hothorn, L.A. / Santiago, J.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: 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_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Protein IDA
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Protein IDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,87740
Polymers180,2616
Non-polymers9,61634
Water6,521362
1
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Protein IDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,84220
Polymers90,1303
Non-polymers4,71217
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Protein IDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,03420
Polymers90,1303
Non-polymers4,90417
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.332, 145.878, 169.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21DDD
32BBB
42EEE
53CCC
63FFF

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEUAAAA13 - 6052 - 594
211SERSERLEULEUDDDD13 - 6052 - 594
322ASNASNPROPROBBBB27 - 2118 - 192
422ASNASNPROPROEEEE27 - 2118 - 192
533TYRTYRASNASNCCCC56 - 691 - 14
633TYRTYRASNASNFFFF56 - 691 - 14

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 2 types, 4 molecules AAADDDBBBEEE

#1: Protein Receptor-like protein kinase HSL1 / Protein HAESA-LIKE1


Mass: 66569.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HSL1, At1g28440, F3M18.12 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9SGP2, non-specific serine/threonine protein kinase
#2: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 21978.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK1, At1g71830, F14O23.21, F14O23_24 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Protein/peptide , 1 types, 2 molecules CCCFFF

#3: Protein/peptide Protein IDA / Protein INFLORESCENCE DEFICIENT IN ABSCISSION


Mass: 1581.793 Da / Num. of mol.: 2 / Fragment: unp RESIDUES 56-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDA, At1g68765, F14K14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8LAD7

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Sugars , 4 types, 27 molecules

#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.: 3
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)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 11
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
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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.: 12
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, 369 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mg
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M K/Na tartrate 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 7, 2019
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→110.604 Å / Num. obs: 106364 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.998 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.09 / Rrim(I) all: 0.332 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
12.65-110.5822.50.077710.9980.020.072
2.31-2.3526.73.51851460.7030.9813.652

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
xia2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IXO

5ixo


Resolution: 2.31→110.58 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.916 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.304 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.275 5326 5.013 %
Rwork0.2546 100921 -
all0.256 --
obs-106247 99.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.702 Å2
Baniso -1Baniso -2Baniso -3
1-6.324 Å2-0 Å20 Å2
2---2.049 Å2-0 Å2
3----4.274 Å2
Refinement stepCycle: LAST / Resolution: 2.31→110.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11809 0 624 362 12795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01312754
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711664
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1110.1191805
X-RAY DIFFRACTIONr_angle_refined_deg1.251.69617473
X-RAY DIFFRACTIONr_angle_other_deg1.281.6327010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425.0171811
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg17.1462059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44125.298521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65315.3331997
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.957201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7091531
X-RAY DIFFRACTIONr_chiral_restr0.0560.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022570
X-RAY DIFFRACTIONr_nbd_refined0.1760.22271
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.211144
X-RAY DIFFRACTIONr_nbtor_refined0.1550.26311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2416
X-RAY DIFFRACTIONr_metal_ion_refined0.1790.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.216
X-RAY DIFFRACTIONr_nbd_other0.1650.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.216
X-RAY DIFFRACTIONr_mcbond_it3.1634.4116356
X-RAY DIFFRACTIONr_mcbond_other3.1634.4116355
X-RAY DIFFRACTIONr_mcangle_it4.796.6197939
X-RAY DIFFRACTIONr_mcangle_other4.796.6187940
X-RAY DIFFRACTIONr_scbond_it3.8964.9996398
X-RAY DIFFRACTIONr_scbond_other3.8954.9996398
X-RAY DIFFRACTIONr_scangle_it5.9187.3649532
X-RAY DIFFRACTIONr_scangle_other5.9187.3649532
X-RAY DIFFRACTIONr_lrange_it8.16164.495194550
X-RAY DIFFRACTIONr_lrange_other8.159164.508194525
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.0518107
X-RAY DIFFRACTIONr_ncsr_local_group_20.0610.055763
X-RAY DIFFRACTIONr_ncsr_local_group_30.1170.05297
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.060420.05009
12DDDX-RAY DIFFRACTIONLocal ncs0.060420.05009
23BBBX-RAY DIFFRACTIONLocal ncs0.061150.0501
24EEEX-RAY DIFFRACTIONLocal ncs0.061150.0501
35CCCX-RAY DIFFRACTIONLocal ncs0.116520.05005
36FFFX-RAY DIFFRACTIONLocal ncs0.116520.05005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.31-2.370.4543660.42973840.4377560.3350.3599.92260.401
2.37-2.4350.3923870.39672170.39676040.5170.5061000.362
2.435-2.5050.3693610.36569760.36673390.5310.52399.97270.335
2.505-2.5830.3883750.34667770.34871520.5550.6061000.318
2.583-2.6670.3553400.33265970.33369390.6710.69399.97120.303
2.667-2.7610.3173510.29663800.29867310.7880.7871000.268
2.761-2.8650.2913080.28262360.28265450.8460.84899.98470.251
2.865-2.9820.2853280.27559020.27662310.8570.86699.98390.247
2.982-3.1140.2922970.27457310.27560280.8570.8621000.244
3.114-3.2660.2773110.25454390.25557500.8870.9021000.228
3.266-3.4430.2762740.25152260.25355010.890.90799.98180.229
3.443-3.6510.2612930.2448890.24151820.9220.921000.224
3.651-3.9030.2462360.21846790.2249150.9330.9351000.203
3.903-4.2150.2332230.19343370.19545610.9390.95299.97810.181
4.215-4.6170.172010.1640300.1642320.9660.96899.97640.155
4.617-5.1610.1891750.16436630.16538380.9580.971000.163
5.161-5.9570.2371770.21432200.21533980.9420.95199.97060.206
5.957-7.2910.2091460.227580.20129040.9510.9541000.201
7.291-10.2880.261120.23121930.23323050.9280.941000.237
10.288-110.6040.25650.2612870.2613530.9620.94799.92610.276

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