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- PDB-8qtc: Crystal structure of Arabidopsis thaliana 14-3-3 omega in complex... -

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Basic information

Entry
Database: PDB / ID: 8qtc
TitleCrystal structure of Arabidopsis thaliana 14-3-3 omega in complex with a phosphopeptide from the transcription factor BZR1.
Components
  • 14-3-3-like protein GF14 omega
  • Protein BRASSINAZOLE-RESISTANT 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / brassinosteroid / transcription factor / BZR1 / phosphopeptide / signal transduction / plant growth
Function / homology
Function and homology information


brassinosteroid mediated signaling pathway / plant-type vacuole / Golgi apparatus / mitochondrion / nucleus / cytosol
Similarity search - Function
14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
: / 14-3-3-like protein GF14 omega
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHothorn, M. / Obergfell, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: Plant Cell.Physiol. / Year: 2024
Title: Mechanistic Insights into the Function of 14-3-3 Proteins as Negative Regulators of Brassinosteroid Signaling in Arabidopsis.
Authors: Obergfell, E. / Hohmann, U. / Moretti, A. / Chen, H. / Hothorn, M.
History
DepositionOct 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3-like protein GF14 omega
C: Protein BRASSINAZOLE-RESISTANT 1
B: 14-3-3-like protein GF14 omega
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4379
Polymers54,8983
Non-polymers5396
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-66 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.503, 131.503, 256.357
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 213 or (resid 214...
d_2ens_1(chain "B" and resid 3 through 235)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 235 / Label seq-ID: 3 - 235

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BC

NCS oper: (Code: givenMatrix: (-0.757960476169, -0.649309709613, 0.0623924480031), (-0.649173983086, 0.741515285845, -0.169494013292), (0.063789154636, -0.168973317007, -0.983554249592)Vector: -4. ...NCS oper: (Code: given
Matrix: (-0.757960476169, -0.649309709613, 0.0623924480031), (-0.649173983086, 0.741515285845, -0.169494013292), (0.063789154636, -0.168973317007, -0.983554249592)
Vector: -4.42702240473, -8.15035617291, -61.1950991932)

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Components

#1: Protein 14-3-3-like protein GF14 omega


Mass: 27171.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: GRF2 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: Q01525
#2: Protein/peptide Protein BRASSINAZOLE-RESISTANT 1


Mass: 554.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: BZR1 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M (NH4)2SO4 , 10 mM CoCl2 6 H2O, 0.1 M Mes (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999999406361 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999406361 Å / Relative weight: 1
ReflectionResolution: 3.5→68.35 Å / Num. obs: 17253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 38.3 % / Biso Wilson estimate: 142.23 Å2 / CC1/2: 1 / Rrim(I) all: 0.339 / Net I/σ(I): 14.32
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 39.6 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 2692 / CC1/2: 0.37 / Rrim(I) all: 5.05

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→68.35 Å / SU ML: 0.5213 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 863 5 %
Rwork0.2167 16386 -
obs0.2184 17249 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.45 Å2
Refinement stepCycle: LAST / Resolution: 3.5→68.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 26 1 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533852
X-RAY DIFFRACTIONf_angle_d1.04055198
X-RAY DIFFRACTIONf_chiral_restr0.051572
X-RAY DIFFRACTIONf_plane_restr0.009673
X-RAY DIFFRACTIONf_dihedral_angle_d4.3552529
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.3338746232 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.720.36661390.33882640X-RAY DIFFRACTION99.53
3.72-40.29361400.272672X-RAY DIFFRACTION100
4-4.410.22561420.21472683X-RAY DIFFRACTION100
4.41-5.040.25791420.21282710X-RAY DIFFRACTION99.96
5.05-6.360.28491450.25012747X-RAY DIFFRACTION99.97
6.36-68.350.21941550.18082934X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.1484139794 Å / Origin y: -48.6865558576 Å / Origin z: -25.9408263021 Å
111213212223313233
T1.08908584327 Å2-0.018784168812 Å20.153109751743 Å2-1.21215087678 Å20.0872425878415 Å2--1.21807834878 Å2
L3.06874744666 °20.178110824612 °2-1.15832669057 °2-2.01161116854 °2-0.976411628445 °2--2.28333041533 °2
S-0.012286795886 Å °0.394004203839 Å °0.165063077587 Å °0.348294179432 Å °-0.0982931435569 Å °-0.0192613795781 Å °-0.268054858 Å °0.038699708337 Å °0.112107634853 Å °
Refinement TLS groupSelection details: all

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