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- PDB-4lsc: Isolated SERK1 co-receptor ectodomain at high resolution -

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Basic information

Entry
Database: PDB / ID: 4lsc
TitleIsolated SERK1 co-receptor ectodomain at high resolution
ComponentsSomatic embryogenesis receptor kinase 1
KeywordsPROTEIN BINDING / LRR-domain / membrane co-receptor / brassinosteroid binding / N-glycosylation
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 / receptor serine/threonine kinase binding / Golgi organization / histone H3Y41 kinase activity / histone H2AXY142 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 / receptor serine/threonine kinase binding / Golgi organization / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / signaling receptor binding / protein serine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / ATP binding / identical protein 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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase ...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 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. / 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 / Alpha Beta
Similarity search - Domain/homology
Somatic embryogenesis receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 1.529 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 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Somatic embryogenesis receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5554
Polymers24,3801
Non-polymers1,1753
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.630, 72.630, 80.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 24380.256 Da / Num. of mol.: 1
Fragment: receptor ectodomain/LRR-domain (UNP residues 29-788)
Mutation: N115D, N163Q
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
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.7 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.97794
SYNCHROTRONSLS X10SA21.90021
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 18, 2013
DECTRIS PILATUS 6M2PIXELMay 18, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.977941
21.900211
ReflectionResolution: 1.529→49.7 Å / Num. all: 36620 / Num. obs: 36620 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.072 / Net I/σ(I): 16.12
Reflection shellResolution: 1.529→1.57 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.15 / Rsym value: 0.957 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1334)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 1OGQ

1ogq


Resolution: 1.529→49.673 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 1830 5 %
Rwork0.1674 --
obs0.1679 36613 99.97 %
all-36620 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.529→49.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 77 148 1624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091575
X-RAY DIFFRACTIONf_angle_d1.4212183
X-RAY DIFFRACTIONf_dihedral_angle_d20.259596
X-RAY DIFFRACTIONf_chiral_restr0.076280
X-RAY DIFFRACTIONf_plane_restr0.007275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5292-1.57050.23941240.2312681X-RAY DIFFRACTION100
1.5705-1.61670.25541560.21772673X-RAY DIFFRACTION100
1.6167-1.66890.20361500.19032615X-RAY DIFFRACTION100
1.6689-1.72860.19091240.18342708X-RAY DIFFRACTION100
1.7286-1.79780.20581330.18052667X-RAY DIFFRACTION100
1.7978-1.87960.19551410.16682664X-RAY DIFFRACTION100
1.8796-1.97870.18841230.16252689X-RAY DIFFRACTION100
1.9787-2.10270.17481300.14942674X-RAY DIFFRACTION100
2.1027-2.2650.15261450.14852692X-RAY DIFFRACTION100
2.265-2.4930.16291490.15312651X-RAY DIFFRACTION100
2.493-2.85370.19421480.16332684X-RAY DIFFRACTION100
2.8537-3.59520.16581530.16892676X-RAY DIFFRACTION100
3.5952-49.6990.17081540.1712709X-RAY DIFFRACTION100
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)
12.71381.1111-0.82383.5699-0.28391.6362-0.19590.5008-0.1223-0.55750.2095-0.00810.3184-0.0328-0.02060.2932-0.0391-0.00030.2721-0.02120.16751.24057.17710.992
23.2713-0.57391.27931.25261.22652.32570.01790.6408-1.3299-0.5678-0.1270.23971.0679-0.29950.01410.6143-0.0720.02980.2506-0.1210.386244.5592-5.813413.6976
31.42950.04860.05392.19280.49182.5887-0.05020.0089-0.0571-0.0195-0.0040.1430.2088-0.09230.05310.1246-0.00120.00350.10940.00740.135644.78378.763228.2971
45.62010.91221.13745.560.79733.41830.0939-0.3937-0.01210.6205-0.12910.30590.5018-0.09660.02670.28980.00020.06790.1984-0.01730.143642.429511.628444.2822
55.22610.29561.96932.26031.92792.56260.0186-0.4509-0.13621.1022-0.42540.04620.29210.39990.39780.67730.04460.15940.38080.04180.394239.59715.504151.7768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 27:66)
2X-RAY DIFFRACTION2(chain A and resseq 67:72)
3X-RAY DIFFRACTION3(chain A and resseq 73:175)
4X-RAY DIFFRACTION4(chain A and resseq 176:201)
5X-RAY DIFFRACTION5(chain A and resseq 202:212)

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