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- PDB-7odk: Plant peptide hormone receptor H1 -

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Basic information

Entry
Database: PDB / ID: 7odk
TitlePlant peptide hormone receptor H1
ComponentsReceptor-like protein kinase HSL1
KeywordsPEPTIDE BINDING PROTEIN / Plant receptor LRR pepide hormone
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / 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-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...: / 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-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
Receptor-like protein kinase HSL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 29, 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
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
AAA: Receptor-like protein kinase HSL1
BBB: Receptor-like protein kinase HSL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,98246
Polymers133,1402
Non-polymers9,84244
Water12,106672
1
AAA: Receptor-like protein kinase HSL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,58423
Polymers66,5701
Non-polymers5,01422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Receptor-like protein kinase HSL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,39823
Polymers66,5701
Non-polymers4,82922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.539, 84.001, 89.061
Angle α, β, γ (deg.)99.178, 113.727, 108.410
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 18 - 600 / Label seq-ID: 7 - 589

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#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

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Sugars , 5 types, 20 molecules

#2: 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
#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.: 9
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 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}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.: 6 / 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

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Non-polymers , 4 types, 696 molecules

#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium sulfate 0.1 M citric acid pH 4.0 30% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2019
RadiationMonochromator: double-channel cut fixed-exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.83→47.084 Å / Num. obs: 158310 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.06 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.02-47.083.50.01396610.0130.019
1.83-1.863.60.5976950.7210.590.834

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Processing

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

5ixo


Resolution: 1.83→47.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.248 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2164 8013 5.062 %
Rwork0.2044 150297 -
all0.205 --
obs-158310 97.392 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.733 Å2-0.079 Å2-0.127 Å2
2--1.131 Å2-1.075 Å2
3---0.443 Å2
Refinement stepCycle: LAST / Resolution: 1.83→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8798 0 643 672 10113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139759
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179053
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0760.1134939
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.70813290
X-RAY DIFFRACTIONr_angle_other_deg1.2831.64120987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.77451368
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg34.5232055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2424.863401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515.3231581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7851529
X-RAY DIFFRACTIONr_chiral_restr0.0460.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021949
X-RAY DIFFRACTIONr_nbd_refined0.1790.21748
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.28625
X-RAY DIFFRACTIONr_nbtor_refined0.1560.24769
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2576
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.229
X-RAY DIFFRACTIONr_nbd_other0.210.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4180.21
X-RAY DIFFRACTIONr_mcbond_it0.6742.9894759
X-RAY DIFFRACTIONr_mcbond_other0.6742.9884758
X-RAY DIFFRACTIONr_mcangle_it1.2014.4755968
X-RAY DIFFRACTIONr_mcangle_other1.2014.4765969
X-RAY DIFFRACTIONr_scbond_it1.2053.3185000
X-RAY DIFFRACTIONr_scbond_other1.2053.3114992
X-RAY DIFFRACTIONr_scangle_it1.6694.8997322
X-RAY DIFFRACTIONr_scangle_other1.6694.8877311
X-RAY DIFFRACTIONr_lrange_it3.375109.85137857
X-RAY DIFFRACTIONr_lrange_other3.363109.893137736
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.0518705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.045340.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.045340.0501
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
1.83-1.8770.2915940.297109220.297119860.7060.70896.07880.295
1.877-1.9290.2815590.283107290.283117220.7330.73996.29760.278
1.929-1.9850.2665550.26104350.26113850.8340.83196.53050.249
1.985-2.0460.2564950.244102690.245111210.8540.8796.78990.229
2.046-2.1130.2515450.23397580.234106340.8740.88796.88730.215
2.113-2.1870.2435160.22796200.228104260.8980.89997.21850.206
2.187-2.2690.2284940.21892270.21899790.9120.91397.41460.197
2.269-2.3610.2294860.21289490.21396620.9170.92697.65060.19
2.361-2.4660.2154910.21284860.21291990.9270.9397.58670.189
2.466-2.5860.2434550.20981620.21188070.9150.9397.84260.185
2.586-2.7250.2234180.20578190.20684150.9330.93497.88470.185
2.725-2.890.244280.20773490.20979480.9270.93497.84850.188
2.89-3.0890.2193870.20869690.20974790.9320.93898.35540.192
3.089-3.3350.2083380.19864420.19969000.9390.94398.26090.19
3.335-3.6520.2113070.19460130.19564410.9440.94898.12140.193
3.652-4.080.1792410.17354140.17457680.9580.9698.04090.182
4.08-4.7050.1682650.15547350.15551130.9670.97197.78990.17
4.705-5.7480.1962070.18140420.18243110.9630.96598.56180.203
5.748-8.0690.2391400.20931790.2133530.9460.95198.9860.228
8.069-47.0840.149920.20417780.20118930.9680.95998.7850.24

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