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- PDB-7ogz: Plant peptide hormone receptor complex H1L3S1 -

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Basic information

Entry
Database: PDB / ID: 7ogz
TitlePlant peptide hormone receptor complex H1L3S1
Components
  • Peptide hormone IDL3
  • 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


microsporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / apoplast / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity ...microsporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / apoplast / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / non-specific serine/threonine protein kinase / phosphorylation / protein phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular space / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic 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
Protein IDA-LIKE 3 / 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: 2.7 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
DepositionMay 7, 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: Peptide hormone IDL3
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Peptide hormone IDL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,72623
Polymers179,2036
Non-polymers6,52317
Water41423
1
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Peptide hormone IDL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,54911
Polymers89,6023
Non-polymers2,9488
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint32 kcal/mol
Surface area30880 Å2
MethodPISA
2
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Peptide hormone IDL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,17712
Polymers89,6023
Non-polymers3,5759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint37 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.838, 144.501, 168.432
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
111METMETCYSCYSAAAA15 - 6064 - 595
211METMETCYSCYSDDDD15 - 6064 - 595
322ASNASNPROPROBBBB27 - 2118 - 192
422ASNASNPROPROEEEE27 - 2118 - 192
533PROPROASNASNCCCC79 - 901 - 12
633PROPROASNASNFFFF79 - 901 - 12

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: 21736.438 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 / Non-polymers , 2 types, 25 molecules CCCFFF

#3: Protein/peptide Peptide hormone IDL3 / Peptide from protein IDA-LIKE 3


Mass: 1295.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDL3, At5g09805, F17I14, MYH9 / Production host: synthetic construct (others) / References: UniProt: Q6DUW7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 17 molecules

#4: 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.: 10
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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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)][a-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.: 5 / 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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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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M magnesium chloride 0.1 M HEPES pH 7.5 25 % 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: 1.000029 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 11, 2019
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000029 Å / Relative weight: 1
ReflectionResolution: 2.7→48.17 Å / Num. obs: 60957 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.149 / Rrim(I) all: 0.35 / Net I/σ(I): 5.7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.965 / Num. unique obs: 4464 / CC1/2: 0.821 / Rpim(I) all: 0.9 / Rrim(I) all: 2.164

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
xia2data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IXO

5ixo


Resolution: 2.7→47.657 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.855 / SU B: 39.798 / SU ML: 0.705 / Cross valid method: FREE R-VALUE / ESU R: 1.087 / ESU R Free: 0.465
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3708 3065 5.036 %
Rwork0.3526 57798 -
all0.354 --
obs-60863 99.82 %
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: 48.532 Å2
Baniso -1Baniso -2Baniso -3
1-7.128 Å2-0 Å20 Å2
2---0.13 Å2-0 Å2
3----6.998 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11587 0 428 23 12038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01312306
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711199
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0760.1201165
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.67516854
X-RAY DIFFRACTIONr_angle_other_deg1.3271.61325866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835.0351719
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg20.382043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96325.349501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42615.2581878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0041529
X-RAY DIFFRACTIONr_chiral_restr0.0540.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214049
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022511
X-RAY DIFFRACTIONr_nbd_refined0.1830.22392
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.211124
X-RAY DIFFRACTIONr_nbtor_refined0.1590.26239
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.215
X-RAY DIFFRACTIONr_nbd_other0.2350.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.25
X-RAY DIFFRACTIONr_mcbond_it1.7465.2676298
X-RAY DIFFRACTIONr_mcbond_other1.7475.2686297
X-RAY DIFFRACTIONr_mcangle_it3.0317.8957862
X-RAY DIFFRACTIONr_mcangle_other3.0317.8957863
X-RAY DIFFRACTIONr_scbond_it1.5735.5016008
X-RAY DIFFRACTIONr_scbond_other1.5735.5016008
X-RAY DIFFRACTIONr_scangle_it2.5998.2068992
X-RAY DIFFRACTIONr_scangle_other2.5998.2068992
X-RAY DIFFRACTIONr_lrange_it8.455198.339202039
X-RAY DIFFRACTIONr_lrange_other8.455198.34202034
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.0517791
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.055648
X-RAY DIFFRACTIONr_ncsr_local_group_30.0560.05201
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.073380.05008
12DDDX-RAY DIFFRACTIONLocal ncs0.073380.05008
23BBBX-RAY DIFFRACTIONLocal ncs0.070130.05009
24EEEX-RAY DIFFRACTIONLocal ncs0.070130.05009
35CCCX-RAY DIFFRACTIONLocal ncs0.056280.05009
36FFFX-RAY DIFFRACTIONLocal ncs0.056280.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.8460.4822050.4454097X-RAY DIFFRACTION99.8144
2.846-2.9280.4532040.4383991X-RAY DIFFRACTION99.8334
2.928-3.0180.462160.4393881X-RAY DIFFRACTION99.8294
3.018-3.1160.4431970.4233781X-RAY DIFFRACTION99.8243
3.116-3.2250.4571820.4143639X-RAY DIFFRACTION99.8693
3.225-3.3460.4331790.4043538X-RAY DIFFRACTION99.9194
3.346-3.4820.4011950.3873388X-RAY DIFFRACTION99.9442
3.482-3.6360.3981720.3543254X-RAY DIFFRACTION99.9125
3.636-3.8120.3591740.3493116X-RAY DIFFRACTION99.9089
3.812-4.0170.3951510.3412991X-RAY DIFFRACTION99.746
4.017-4.2590.3181550.3092830X-RAY DIFFRACTION99.766
4.259-4.5510.3061360.2872660X-RAY DIFFRACTION99.9642
4.551-4.9120.321440.2762472X-RAY DIFFRACTION99.8473
4.912-5.3750.3211370.2892282X-RAY DIFFRACTION99.7937
5.375-60.3251190.3182112X-RAY DIFFRACTION99.9552
6-6.910.3071030.281851X-RAY DIFFRACTION99.7448
6.91-8.420.3860.2841600X-RAY DIFFRACTION99.8224
8.42-11.730.31660.2811275X-RAY DIFFRACTION99.8511

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