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- PDB-4lsx: Plant steroid receptor ectodomain bound to brassinolide and SERK1... -

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Basic information

Entry
Database: PDB / ID: 4lsx
TitlePlant steroid receptor ectodomain bound to brassinolide and SERK1 co-receptor ectodomain
Components
  • Protein BRASSINOSTEROID INSENSITIVE 1
  • Somatic embryogenesis receptor kinase 1
KeywordsSTEROID BINDING PROTEIN/PROTEIN BINDING / LRR-domain / membrane signaling complex receptor co-receptor complex / brassinosteroid binding / N-glycosylation / STEROID BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


microsporogenesis / detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / floral organ abscission / pollen exine formation / pollen maturation / seedling development / skotomorphogenesis / positive regulation of flower development ...microsporogenesis / detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / floral organ abscission / pollen exine formation / pollen maturation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / microtubule bundle formation / response to UV-B / Golgi organization / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / endosome membrane / non-specific serine/threonine protein kinase / endosome / protein kinase activity / protein heterodimerization activity / phosphorylation / signaling receptor binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Dna Ligase; domain 1 - #310 / Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...Dna Ligase; domain 1 - #310 / Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Brassinolide / Protein BRASSINOSTEROID INSENSITIVE 1 / Somatic embryogenesis receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsSantiago, J. / Henzler, C. / Hothorn, M.
CitationJournal: Science / Year: 2013
Title: Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases.
Authors: Santiago, J. / Henzler, C. / Hothorn, M.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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: Protein BRASSINOSTEROID INSENSITIVE 1
B: Protein BRASSINOSTEROID INSENSITIVE 1
C: Somatic embryogenesis receptor kinase 1
D: Somatic embryogenesis receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,28420
Polymers211,1824
Non-polymers7,10216
Water0
1
A: Protein BRASSINOSTEROID INSENSITIVE 1
C: Somatic embryogenesis receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,04110
Polymers105,5912
Non-polymers3,4498
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein BRASSINOSTEROID INSENSITIVE 1
D: Somatic embryogenesis receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,24410
Polymers105,5912
Non-polymers3,6538
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.896, 69.896, 873.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Protein BRASSINOSTEROID INSENSITIVE 1 / AtBRI1 / Brassinosteroid LRR receptor kinase


Mass: 83726.594 Da / Num. of mol.: 2
Fragment: receptor ectodomain/LRR-domain (UNP residues 29-788)
Mutation: G643E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: col 0 / Gene: At4g39400, BRI1, F23K16.30 / Plasmid: pBAC-6 mod. / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao38 / References: UniProt: O22476
#2: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 21864.566 Da / Num. of mol.: 2
Fragment: co-receptor kinase ectodomain/LRR-domain (UNP residues 24-213)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: col 0 / Gene: At1g71830, F14O23.21, F14O23_24, SERK1 / Plasmid: pBAC-6 mod. / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao38 / References: UniProt: Q94AG2

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Sugars , 5 types, 14 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 2
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
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-4]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(4+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 1
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
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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 , 1 types, 2 molecules

#7: Chemical ChemComp-BLD / Brassinolide / (3aS,5S,6R,7aR,7bS,9aS,10R,12aS,12bS)-10-[(2S,3R,4R,5S)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-5,6-dihydroxy-7a,9a-dime thylhexadecahydro-3H-benzo[c]indeno[5,4-e]oxepin-3-one / Brassinolide


Mass: 480.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H48O6 / Comment: hormone*YM

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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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 22% PEG3350, 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 3.3→48.53 Å / Num. all: 35235 / Num. obs: 35235 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.67 % / Rmerge(I) obs: 0.121 / Rsym value: 0.112 / Net I/σ(I): 12.16
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 6.12 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.34 / Rsym value: 0.691 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1334)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4LSA AND 4LSC

4lsa

4lsc


Resolution: 3.302→48.53 Å / σ(F): 1.38 / Phase error: 31.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2848 2040 5.79 %
Rwork0.2463 --
obs0.2484 35233 98.15 %
all-35235 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.302→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13448 0 472 0 13920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314229
X-RAY DIFFRACTIONf_angle_d0.88319406
X-RAY DIFFRACTIONf_dihedral_angle_d16.8615150
X-RAY DIFFRACTIONf_chiral_restr0.0362371
X-RAY DIFFRACTIONf_plane_restr0.0052467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3032-3.38580.34431340.32662263X-RAY DIFFRACTION91
3.3858-3.47730.38451540.31272394X-RAY DIFFRACTION91
3.4773-3.57960.32311420.30682321X-RAY DIFFRACTION92
3.5796-3.6950.28921480.27782451X-RAY DIFFRACTION93
3.695-3.8270.2541400.26792325X-RAY DIFFRACTION93
3.827-3.98010.32321370.26842374X-RAY DIFFRACTION93
3.9801-4.16110.24871400.23612439X-RAY DIFFRACTION94
4.1611-4.38020.31291490.22472416X-RAY DIFFRACTION93
4.3802-4.65430.24751440.21952386X-RAY DIFFRACTION92
4.6543-5.0130.26581400.2122382X-RAY DIFFRACTION93
5.013-5.51640.32451440.22732340X-RAY DIFFRACTION93
5.5164-6.31210.29161480.24432379X-RAY DIFFRACTION92
6.3121-7.94270.26551360.23352371X-RAY DIFFRACTION93
7.9427-40.54510.26961540.24792349X-RAY DIFFRACTION91
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)
10.7097-0.04990.14520.53580.10411.6513-0.219-0.8428-0.28840.011-0.08990.09020.02590.51430.08560.44160.2085-0.10910.8703-0.18240.803524.581877.6888-65.1923
20.20660.14110.13090.6828-0.82222.0375-0.4164-0.29650.1062-0.62730.4687-0.03680.3429-0.4224-0.03461.1719-0.227-0.04670.3856-0.05310.692626.194976.3125-117.1919
30.1885-0.20060.39010.7553-0.50361.03230.4999-0.0097-0.1332-0.29410.07540.13880.53120.1299-0.13720.4653-0.07560.00092.473-0.18720.5108-0.839675.9075-37.0762
40.2783-0.1286-0.17270.14070.13650.15090.08520.22950.52170.0390.2426-0.06240.09080.13880.01862.2473-0.7804-0.29740.8589-0.51450.824540.151899.1577-142.9543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 770 )
2X-RAY DIFFRACTION2chain 'B' and (resid 31 through 771 )
3X-RAY DIFFRACTION3chain 'C' and (resid 27 through 211 )
4X-RAY DIFFRACTION4chain 'D' and (resid 27 through 211 )

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