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- PDB-7wq5: Crystal structure of Arabidopsis transcriptional factor WRINKLED1... -

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Basic information

Entry
Database: PDB / ID: 7wq5
TitleCrystal structure of Arabidopsis transcriptional factor WRINKLED1 with dsDNA
Components
  • DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')
  • Ethylene-responsive transcription factor WRI1
KeywordsDNA BINDING PROTEIN / transcriptional factor
Function / homology
Function and homology information


positive regulation of cutin biosynthetic process / triglyceride biosynthetic process / regulation of carbohydrate metabolic process / ethylene-activated signaling pathway / response to sucrose / regulation of glycolytic process / lipid biosynthetic process / lipid metabolic process / kinase binding / DNA-binding transcription factor activity ...positive regulation of cutin biosynthetic process / triglyceride biosynthetic process / regulation of carbohydrate metabolic process / ethylene-activated signaling pathway / response to sucrose / regulation of glycolytic process / lipid biosynthetic process / lipid metabolic process / kinase binding / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
AP2/ERF domain / GCC-box Binding Domain / AP2/ERF domain superfamily / AP2/ERF domain profile. / DNA-binding domain in plant proteins such as APETALA2 and EREBPs / AP2 domain / AP2/ERF domain / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / DNA / DNA (> 10) / Ethylene-responsive transcription factor WRI1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsZhu, Q. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Sci Adv / Year: 2022
Title: Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis.
Authors: Qiao, Z. / Kong, Q. / Tee, W.T. / Lim, A.R.Q. / Teo, M.X. / Olieric, V. / Low, P.M. / Yang, Y. / Qian, G. / Ma, W. / Gao, Y.G.
History
DepositionJan 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethylene-responsive transcription factor WRI1
B: Ethylene-responsive transcription factor WRI1
F: DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')
C: DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9017
Polymers87,8836
Non-polymers181
Water36020
1
A: Ethylene-responsive transcription factor WRI1
C: DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9604
Polymers43,9423
Non-polymers181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-50 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: Ethylene-responsive transcription factor WRI1
F: DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,9423
Polymers43,9423
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-41 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.520, 132.050, 124.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Ethylene-responsive transcription factor WRI1 / Protein ACTIVATOR OF SPORAMIN::LUC 1 / Protein WRINKLED 1


Mass: 29202.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRI1, ASML1, At3g54320, T12E18.10, T12E18.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6X5Y6
#2: DNA chain DNA (5'-D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP*TP*A)-3')


Mass: 7516.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP*AP*C)-3')


Mass: 7222.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 32013 / % possible obs: 99.46 % / Redundancy: 26 % / Biso Wilson estimate: 71.98 Å2 / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 32.27
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 26 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 3176 / CC1/2: 0.708 / Rrim(I) all: 2.85 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.20rc2_4400refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.75 Å / SU ML: 0.4635 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.4836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 1599 5.01 %
Rwork0.2426 30342 -
obs0.2443 31941 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.48 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 1968 1 20 4652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684930
X-RAY DIFFRACTIONf_angle_d0.91327072
X-RAY DIFFRACTIONf_chiral_restr0.0481756
X-RAY DIFFRACTIONf_plane_restr0.0087569
X-RAY DIFFRACTIONf_dihedral_angle_d32.00491329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.45111430.39962720X-RAY DIFFRACTION99.83
2.43-2.510.45231450.40992751X-RAY DIFFRACTION99.76
2.51-2.610.50231440.42022723X-RAY DIFFRACTION99.86
2.61-2.730.42011430.37382722X-RAY DIFFRACTION99.97
2.73-2.880.39431460.3522761X-RAY DIFFRACTION99.73
2.88-3.060.39471430.34572719X-RAY DIFFRACTION99.58
3.06-3.290.36141430.31232707X-RAY DIFFRACTION97.57
3.29-3.620.30581430.26422720X-RAY DIFFRACTION98.66
3.62-4.150.26711460.23782780X-RAY DIFFRACTION99.63
4.15-5.220.22411480.21272809X-RAY DIFFRACTION99.86
5.22-39.750.20531550.17142930X-RAY DIFFRACTION99.97

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