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- PDB-7cvo: crystal structure of Arabidopsis CO CCT domain in complex with NF... -

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Basic information

Entry
Database: PDB / ID: 7cvo
Titlecrystal structure of Arabidopsis CO CCT domain in complex with NF-YB3/YC4 and FT CORE2 DNA
Components
  • Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
  • FT CORE2 DNA forward strand
  • FT CORE2 DNA reverse strand
  • Nuclear transcription factor Y subunit B-3
KeywordsDNA BINDING PROTEIN/DNA / CONSTANS / transcription factor / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / far-red light signaling pathway / regulation of long-day photoperiodism, flowering / positive regulation of photomorphogenesis / CCAAT-binding factor complex / regulation of flower development / gibberellic acid mediated signaling pathway / regulation of seed germination / flower development / response to far red light ...: / far-red light signaling pathway / regulation of long-day photoperiodism, flowering / positive regulation of photomorphogenesis / CCAAT-binding factor complex / regulation of flower development / gibberellic acid mediated signaling pathway / regulation of seed germination / flower development / response to far red light / response to water deprivation / abscisic acid-activated signaling pathway / plastid / positive regulation of protein metabolic process / response to heat / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity / protein heterodimerization activity / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain ...CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear transcription factor Y subunit B-3 / Zinc finger protein CONSTANS / Nuclear transcription factor Y subunit C-4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLv, X. / Du, J.
CitationJournal: Plant Cell / Year: 2021
Title: Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex.
Authors: Lv, X. / Zeng, X. / Hu, H. / Chen, L. / Zhang, F. / Liu, R. / Liu, Y. / Zhou, X. / Wang, C. / Wu, Z. / Kim, C. / He, Y. / Du, J.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-3
D: FT CORE2 DNA forward strand
E: FT CORE2 DNA reverse strand
F: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-3


Theoretical massNumber of molelcules
Total (without water)76,6696
Polymers76,6696
Non-polymers00
Water88349
1
A: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-3
D: FT CORE2 DNA forward strand
E: FT CORE2 DNA reverse strand

F: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-3


Theoretical massNumber of molelcules
Total (without water)76,6696
Polymers76,6696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area17500 Å2
ΔGint-144 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.744, 139.944, 65.569
Angle α, β, γ (deg.)90.000, 108.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS / AtNF-YC-4


Mass: 18933.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFYC4, At5g63470, MLE2.10, CO, At5g15840, F14F8_220 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FMV5, UniProt: Q39057
#2: Protein Nuclear transcription factor Y subunit B-3 / AtNF-YB-3 / Transcriptional activator HAP3C


Mass: 11724.325 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFYB3, HAP3C, At4g14540, dl3310w, FCAALL.252 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O23310
#3: DNA chain FT CORE2 DNA forward strand


Mass: 7752.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: DNA chain FT CORE2 DNA reverse strand


Mass: 7600.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M KI and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28875 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.664 / Num. unique obs: 2851 / CC1/2: 0.83 / CC star: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AWL

4awl


Resolution: 2.6→48.016 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1456 5.08 %
Rwork0.1962 27202 -
obs0.1974 28658 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.31 Å2 / Biso mean: 58.1874 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.6→48.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 1019 0 49 4376
Biso mean---54.52 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154498
X-RAY DIFFRACTIONf_angle_d1.4786260
X-RAY DIFFRACTIONf_chiral_restr0.075707
X-RAY DIFFRACTIONf_plane_restr0.008620
X-RAY DIFFRACTIONf_dihedral_angle_d22.4261817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.69290.26091300.25222721100
2.6929-2.80070.25741380.24652729100
2.8007-2.92820.30691540.24742708100
2.9282-3.08260.32351570.25142732100
3.0826-3.27560.2361500.23282727100
3.2756-3.52850.2431350.21462720100
3.5285-3.88340.23531530.1916267098
3.8834-4.4450.19381320.1668273699
4.445-5.59890.1781380.16942738100
5.5989-480.18381690.1717272199
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)
10.0342-0.13070.1720.643-0.82951.16780.44830.2429-0.0174-0.0311-0.3167-0.96421.13231.82840.3371.21210.1261-0.03751.26550.00741.0352.511-26.889-21.681
27.6426-1.32690.33157.1718-0.90386.5308-0.02340.25760.017-0.01740.2064-0.4637-0.53170.036-0.13060.3312-0.01230.07080.5197-0.0520.412113.411-31.806-12.528
32.16031.59791.26961.648-0.38763.06160.0379-0.30320.08540.854-0.0214-0.06160.18890.2402-0.08860.8419-0.060.03480.6194-0.07120.69933.749-17.46715.79
42.37610.86190.35395.5698-0.3672.46880.04440.03210.04840.1402-0.0065-0.1405-0.03930.1114-0.05970.36740.02130.0380.3234-0.0010.25230.525-33.315-3.958
57.2218-1.7251.07947.3610.37832.9935-0.4898-0.16010.73160.0101-0.14380.7835-0.8874-0.54070.40880.5420.067-0.14170.4767-0.04420.5927-12.234-25.431-8.387
63.05713.1055-3.15186.5146-0.42255.59170.1897-0.89990.00570.8172-0.15310.48460.684-0.03970.06290.6156-0.04340.01640.45780.0230.2931-0.714-29.1944.778
72.02211.09170.05086.07991.72872.7983-0.04710.038-0.0732-0.01540.0411-0.007-0.08180.10480.04740.2813-0.0043-0.02250.33790.02390.2625-2.307-34.808-5.245
84.3421.5379-3.10717.85-2.31337.4847-0.36160.0399-0.6766-0.40970.1076-0.24441.18440.04120.27090.30610.0080.02060.2592-0.02680.3437-0.071-53.162-8.764
95.80551.47940.39723.6712-0.67257.57080.20640.6657-0.3755-0.4843-0.3527-0.71270.5660.84430.00740.51740.0740.00850.5075-0.05040.54798.09-42.28-11.01
101.06021.4436-0.15164.9137-0.81510.75250.2885-0.2130.02010.2595-0.46340.00580.05370.06470.15360.60180.00630.04360.4699-0.01890.4519-1.613-20.43510.287
110.71941.1573-0.21824.5566-0.71591.37510.2402-0.1613-0.02470.5425-0.39630.0709-0.09870.17080.13090.538-0.01540.00240.4918-0.06760.5176-3.86-24.210.75
129.17620.63781.21426.16440.36340.414-0.28750.0482-0.93710.12160.30930.16580.3829-0.51840.07840.4320.0524-0.05520.6792-0.01390.618939.782-40.192-13.091
135.1214-2.5587-2.16647.2581.88066.63080.73091.02060.1173-0.2014-0.6951-0.489-0.0436-0.6755-0.17940.4564-0.001-0.02190.49270.08060.352321.687-27.172-28.671
145.8294-0.38960.39582.611-1.85126.5203-0.13670.5145-0.508-0.1558-0.1102-0.79730.24580.52830.31230.3191-0.01660.01290.5102-0.07950.440332.244-38.755-22.716
153.95130.56590.30442.3704-0.57034.8559-0.24270.2636-1.02250.0826-0.4199-0.14331.19140.52020.53840.61480.07770.1040.51460.01940.737429.126-50.719-16.862
166.85610.5561-0.01635.8697-1.08696.9641-0.32530.2843-0.8708-0.02940.20210.29971.5209-0.3460.18820.5997-0.06890.20240.50480.00360.728815.646-46.524-18.378
171.9735-1.1092.21336.0465-0.33987.39170.27771.4262-0.3561-1.48-0.5021-0.11730.2972-0.62480.26750.67710.05450.09710.7037-0.14520.516827.374-43.242-31.782
183.69392.29350.57874.8493-0.68083.193-0.09340.2142-0.5112-0.39430.0824-0.55890.29320.0463-0.04540.3054-0.00420.04220.471-0.00410.359825.105-37.018-21.6
194.1944-1.16271.27472.64514.06859.0230.1954-0.57391.66630.99590.28060.6048-1.498-0.3636-0.26150.89810.02650.07250.62020.06220.791123.193-14.043-19.724
205.788-1.21321.71642.1736-2.34928.111-0.50530.32931.14270.8570.4012-0.5598-0.97440.4061-0.28170.499-0.0197-0.04790.4565-0.04550.555930.607-22.674-16.455
219.48513.0615-2.74615.8591-0.97624.95420.0752-0.53860.59370.2492-0.4279-0.0757-0.46250.54160.36960.3385-0.0122-0.0460.6514-0.03610.423234.76-30.534-15.88
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 298:302 )A298 - 302
2X-RAY DIFFRACTION2( CHAIN A AND RESID 303:319 )A303 - 319
3X-RAY DIFFRACTION3( CHAIN A AND RESID 320:347 )A320 - 347
4X-RAY DIFFRACTION4( CHAIN B AND RESID 23:94 )B23 - 94
5X-RAY DIFFRACTION5( CHAIN B AND RESID 95:110 )B95 - 110
6X-RAY DIFFRACTION6( CHAIN A AND RESID 77:90 )A77 - 90
7X-RAY DIFFRACTION7( CHAIN A AND RESID 91:126 )A91 - 126
8X-RAY DIFFRACTION8( CHAIN A AND RESID 127:143 )A127 - 143
9X-RAY DIFFRACTION9( CHAIN A AND RESID 144:156 )A144 - 156
10X-RAY DIFFRACTION10( CHAIN D AND RESID 1:25 )D1 - 25
11X-RAY DIFFRACTION11( CHAIN E AND RESID 1:25 )E1 - 25
12X-RAY DIFFRACTION12( CHAIN F AND RESID 300:319 )F300 - 319
13X-RAY DIFFRACTION13( CHAIN G AND RESID 23:46 )G23 - 46
14X-RAY DIFFRACTION14( CHAIN G AND RESID 47:74 )G47 - 74
15X-RAY DIFFRACTION15( CHAIN G AND RESID 75:94 )G75 - 94
16X-RAY DIFFRACTION16( CHAIN G AND RESID 95:110 )G95 - 110
17X-RAY DIFFRACTION17( CHAIN F AND RESID 78:90 )F78 - 90
18X-RAY DIFFRACTION18( CHAIN F AND RESID 91:126 )F91 - 126
19X-RAY DIFFRACTION19( CHAIN F AND RESID 127:133 )F127 - 133
20X-RAY DIFFRACTION20( CHAIN F AND RESID 134:143 )F134 - 143
21X-RAY DIFFRACTION21( CHAIN F AND RESID 144:155 )F144 - 155

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