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- PDB-4m7e: Structural insight into BL-induced activation of the BRI1-BAK1 complex -

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Basic information

Entry
Database: PDB / ID: 4m7e
TitleStructural insight into BL-induced activation of the BRI1-BAK1 complex
Components
  • BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
  • Protein BRASSINOSTEROID INSENSITIVE 1
KeywordsTRANSFERASE / phytohormone / brassinosteroid-insensitive 1 / leucine-rich repeat / receptor-like kinases
Function / homology
Function and homology information


detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / positive regulation of flower development / seedling development / brassinosteroid mediated signaling pathway / leaf development / receptor serine/threonine kinase binding / response to UV-B ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / positive regulation of flower development / seedling development / brassinosteroid mediated signaling pathway / leaf development / receptor serine/threonine kinase binding / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / defense response / receptor protein-tyrosine kinase / non-specific serine/threonine protein kinase / protein kinase activity / endosome / endosome membrane / protein heterodimerization activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Brassinolide / Protein BRASSINOSTEROID INSENSITIVE 1 / BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.602 Å
AuthorsChai, J. / Han, Z. / Sun, Y.
CitationJournal: To be Published
Title: Structural insight into BL-induced activation of the BRI1-BAK1 complex
Authors: Sun, Y. / Han, Z. / Chai, J.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 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_unobs_or_zero_occ_atoms / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
C: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,86315
Polymers209,3484
Non-polymers3,51511
Water00
1
A: Protein BRASSINOSTEROID INSENSITIVE 1
C: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5428
Polymers104,6742
Non-polymers1,8686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein BRASSINOSTEROID INSENSITIVE 1
D: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3217
Polymers104,6742
Non-polymers1,6475
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.911, 145.911, 166.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 2 types, 4 molecules ABDC

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


Mass: 83048.812 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRI1, At4g39400, F23K16.30 / Cell (production host): high five
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor ...AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor kinase 3 / AtSERK3 / Somatic embryogenesis receptor-like kinase 3


Mass: 21625.393 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Cell (production host): high five
References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 2 types, 7 molecules

#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.: 4
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: 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.: 3
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 , 2 types, 4 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: 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


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

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Details

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: 4.88 Å3/Da / Density % sol: 74.8 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4
Details: 0.1M Citric Acid, 2.0M (NH4)2SO4, pH 4.0, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 45864 / Num. obs: 45084 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.061

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGZ

3rgz


Resolution: 3.602→45.904 Å / SU ML: 0.49 / σ(F): 1.97 / Phase error: 33.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 2259 5.03 %RANDOM
Rwork0.2197 ---
obs0.2226 44924 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.602→45.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13694 0 232 0 13926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414207
X-RAY DIFFRACTIONf_angle_d2.09119299
X-RAY DIFFRACTIONf_dihedral_angle_d18.5795220
X-RAY DIFFRACTIONf_chiral_restr0.1352299
X-RAY DIFFRACTIONf_plane_restr0.0112474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6015-3.67980.35271540.2961269697
3.6798-3.76540.36011280.2866266098
3.7654-3.85950.35741580.2822268798
3.8595-3.96380.32671470.2713266898
3.9638-4.08040.33571570.2429267099
4.0804-4.2120.27591420.2192266499
4.212-4.36240.20961500.1965266898
4.3624-4.53690.2171360.1762272399
4.5369-4.74320.31841160.1741268899
4.7432-4.9930.25261220.1727270699
4.993-5.30540.24761320.1879268598
5.3054-5.71430.26231240.2168270199
5.7143-6.28810.28231320.2261269599
6.2881-7.1950.32791510.2128261597
7.195-9.05350.27061470.2502260396
9.0535-45.90740.23251630.2114253694

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