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- PDB-6j9a: Crystal structure of Arabidopsis thaliana VAL1 in complex with FL... -

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Basic information

Entry
Database: PDB / ID: 6j9a
TitleCrystal structure of Arabidopsis thaliana VAL1 in complex with FLC DNA fragment
Components
  • B3 domain-containing transcription repressor VAL1
  • DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')
  • DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / flowering time regulation / DNA-binding / GENE REGULATION / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to sucrose / response to abscisic acid / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. ...DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / B3 domain-containing transcription repressor VAL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.915 Å
AuthorsHu, H. / Du, J.
CitationJournal: Nat.Plants / Year: 2019
Title: Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis.
Authors: Tao, Z. / Hu, H. / Luo, X. / Jia, B. / Du, J. / He, Y.
History
DepositionJan 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B3 domain-containing transcription repressor VAL1
B: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')
C: DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,0093
Polymers24,0093
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.157, 59.157, 97.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein B3 domain-containing transcription repressor VAL1 / Protein HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE 2 / Protein VP1/ABI3-LIKE 1


Mass: 14832.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Plasmid: pSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8W4L5
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3') / FLC CME DNA


Mass: 4615.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3') / FLC CME DNA


Mass: 4562.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M LiCl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 5228 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 27.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 14 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.985 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.915→31.731 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 245 4.69 %
Rwork0.2044 --
obs0.2063 5228 70.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.915→31.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 607 0 0 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011525
X-RAY DIFFRACTIONf_angle_d1.1452190
X-RAY DIFFRACTIONf_dihedral_angle_d31.373610
X-RAY DIFFRACTIONf_chiral_restr0.079242
X-RAY DIFFRACTIONf_plane_restr0.014178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9152-3.6720.3177620.24031478X-RAY DIFFRACTION42
3.672-31.73270.2191830.19073505X-RAY DIFFRACTION100
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)
10.5383-0.5442-0.00240.7749-0.47011.14520.0035-0.09480.11250.05880.09520.049-0.0479-0.17840.17180.03240.0355-0.00030.35890.04040.142215.008360.883746.8669
22.598-0.3497-0.95060.166-0.48193.4775-0.06050.0456-0.3179-0.1070.1276-0.05880.23610.31510.26310.1571-0.00930.13320.1256-0.0510.309213.315147.245747.2007
31.91650.8821-0.0220.4064-0.0290.7063-0.01170.03150.2858-0.04170.11730.2327-0.0702-0.12710.03690.1064-0.0716-0.02320.25370.04310.35222.126159.035240.8946
40.5837-0.38310.49210.7283-0.20070.4465-0.0166-0.0878-0.0477-0.0578-0.0198-0.00580.04640.0694-0.17720.01570.0130.08210.2451-0.03810.224814.177852.649141.1801
50.95390.6883-0.97951.4276-0.06421.4499-0.1318-0.20620.0410.16080.2174-0.25120.13270.4242-0.08330.2248-0.0479-0.05220.27320.00330.184316.130757.662641.7954
63.50661.0356-0.2444.5443-0.08482.52180.0243-0.15010.2408-0.09220.40720.0198-0.0863-0.282-0.25760.1080.0336-0.07360.1660.00060.22979.965867.466945.2142
70.24130.30270.20020.37980.25120.1660.0357-0.8688-0.17840.941-0.06280.38710.1971-0.37110.02280.76360.1727-0.03740.78670.25440.903-3.130354.109651.5336
83.39812.4495-0.29814.1991-0.61471.5106-0.19040.0020.0638-0.19960.1513-0.4501-0.0833-0.08930.00130.18710.14490.01640.2790.0320.3067.545668.097946.7448
90.2002-0.14860.61871.51930.09232.1210.07990.2096-0.1695-0.38760.1433-0.36140.12580.3322-0.03420.2017-0.05270.03760.6147-0.04610.224428.548758.102842.0117
100.94760.28460.58580.96120.03951.77960.08330.2493-0.286-0.13550.332-0.21910.22610.4814-0.29560.174-0.103-0.10590.6486-0.06160.228128.716756.128538.7136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 291 through 319 )
2X-RAY DIFFRACTION2chain 'A' and (resid 320 through 329 )
3X-RAY DIFFRACTION3chain 'A' and (resid 330 through 340 )
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 351 )
5X-RAY DIFFRACTION5chain 'A' and (resid 352 through 369 )
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 381 )
7X-RAY DIFFRACTION7chain 'A' and (resid 382 through 387 )
8X-RAY DIFFRACTION8chain 'A' and (resid 388 through 396 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 15 )

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