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- PDB-5nqv: Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5nqv
TitleStructure of the Arabidopsis Thaliana TOPLESS N-terminal domain
Components
  • EAR motif of IAA27
  • Protein TOPLESS
KeywordsTRANSCRIPTION / TOPLESS / Transcription Factor / Plant / Auxin
Function / homology
Function and homology information


primary shoot apical meristem specification / xylem and phloem pattern formation / jasmonic acid mediated signaling pathway / response to auxin / auxin-activated signaling pathway / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity ...primary shoot apical meristem specification / xylem and phloem pattern formation / jasmonic acid mediated signaling pathway / response to auxin / auxin-activated signaling pathway / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
AUX/IAA protein / Topless family / AUX/IAA domain / AUX/IAA family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / PB1 domain profile. / PB1 domain ...AUX/IAA protein / Topless family / AUX/IAA domain / AUX/IAA family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / PB1 domain profile. / PB1 domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Protein TOPLESS / Auxin-responsive protein IAA27
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNanao, M.H. / Arevalillo, M.R. / Vinos-Poyo, T. / Parcy, F. / Dumas, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression.
Authors: Martin-Arevalillo, R. / Nanao, M.H. / Larrieu, A. / Vinos-Poyo, T. / Mast, D. / Galvan-Ampudia, C. / Brunoud, G. / Vernoux, T. / Dumas, R. / Parcy, F.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 TOPLESS
B: Protein TOPLESS
C: Protein TOPLESS
D: Protein TOPLESS
E: EAR motif of IAA27
F: EAR motif of IAA27
G: EAR motif of IAA27
H: EAR motif of IAA27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,01318
Polymers105,8618
Non-polymers1,15310
Water9,548530
1
A: Protein TOPLESS
C: Protein TOPLESS
E: EAR motif of IAA27
G: EAR motif of IAA27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65710
Polymers52,9304
Non-polymers7276
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-38 kcal/mol
Surface area20420 Å2
MethodPISA
2
B: Protein TOPLESS
D: Protein TOPLESS
F: EAR motif of IAA27
H: EAR motif of IAA27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3578
Polymers52,9304
Non-polymers4264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-32 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 94.100, 298.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Protein TOPLESS / WUS-interacting protein 1


Mass: 25292.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPL, WSIP1, At1g15750, F7H2.9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta De3 / References: UniProt: Q94AI7
#2: Protein/peptide
EAR motif of IAA27


Mass: 1172.310 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9ZSY8*PLUS
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Di-Ammonium tartrate 1.08 M pH 7 and 2% benzamidine-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 96754 / Num. obs: 709778 / % possible obs: 98.1 % / Redundancy: 7.33 % / Biso Wilson estimate: 39.07 Å2 / CC1/2: 0.999 / Rsym value: 0.091 / Net I/σ(I): 13.12
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 7.57 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 15208 / Num. unique obs: 115219 / CC1/2: 0.551 / Rsym value: 1.963 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION November 3, 2014data reduction
XSCALEVERSION November 3, 2014data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NQS

5nqs


Resolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4831 5 %RANDOM
Rwork0.19 ---
obs0.191 96694 98.2 %-
Displacement parametersBiso mean: 50.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.4045 Å20 Å20 Å2
2---2.4045 Å20 Å2
3---4.8089 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 76 530 6957
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016539HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.938750HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2468SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes202HARMONIC2
X-RAY DIFFRACTIONt_gen_planes913HARMONIC5
X-RAY DIFFRACTIONt_it6539HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion16.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion805SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7780SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 325 4.7 %
Rwork0.373 6588 -
all0.374 6913 -
obs--96.35 %
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)
11.52570.4643-0.96420.0784-0.47331.2497-0.12870.1764-0.0615-0.03820.09590.03330.1278-0.07720.03270.0158-0.03620.0215-0.04050.0507-0.0473-13.7799-39.602338.9735
21.3095-0.59381.14890.6012-0.64562.2125-0.0474-0.21260.08060.05310.04660.009-0.2144-0.10070.0008-0.0284-0.04720.0239-0.01580.034-0.1056-19.9856-54.899387.8867
30.5068-0.0915-0.00111.8162-1.15851.3555-0.0301-0.10080.07370.38-0.0358-0.1277-0.02330.07590.06590.0704-0.0301-0.0479-0.05010.0394-0.159414.5273-34.840745.545
42.10020.562-0.69961.4198-0.57532.3647-0.11090.0785-0.2446-0.34960.0941-0.00890.3983-0.03060.01680.0494-0.0171-0.0031-0.15790.0015-0.16744.8013-70.375983.6448
50.46110.10170.05520.2910.07870.2135-0.00920.0294-0.0164-0.00930.0097-0.00710.0319-0.0376-0.00060.00760.00040.0418-0.0540.10830.0528-30.0289-43.774444.5596
60-0.02270.020-0.02280.00330.00020.00170.00040.0015-0.001-0.0041-0.00110.00180.0008-0.0028-0.0006-0.00250.00690.0001-0.002927.6938-45.022457.1014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|179 }
2X-RAY DIFFRACTION2{ B|2 - B|179 }
3X-RAY DIFFRACTION3{ C|-9 - C|180 }
4X-RAY DIFFRACTION4{ D|2 - D|178 }
5X-RAY DIFFRACTION5{ E|7 - E|16 }
6X-RAY DIFFRACTION6{ G|8 - G|11 }

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