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- PDB-6j9b: Arabidopsis FUS3-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6j9b
TitleArabidopsis FUS3-DNA complex
Components
  • B3 domain-containing transcription factor FUS3
  • 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 / DNA-binding / B3 domain / flowering regulation / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of abscisic acid biosynthetic process / negative regulation of gibberellin biosynthetic process / somatic embryogenesis / plant organ development / positive regulation of abscisic acid-activated signaling pathway / vegetative to reproductive phase transition of meristem / response to auxin / embryo development ending in seed dormancy / regulation of embryonic development / kinase binding ...positive regulation of abscisic acid biosynthetic process / negative regulation of gibberellin biosynthetic process / somatic embryogenesis / plant organ development / positive regulation of abscisic acid-activated signaling pathway / vegetative to reproductive phase transition of meristem / response to auxin / embryo development ending in seed dormancy / regulation of embryonic development / kinase binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / DNA 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / B3 domain-containing transcription factor FUS3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.1Nov 22, 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: B3 domain-containing transcription factor FUS3
C: DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')
B: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')
D: B3 domain-containing transcription factor FUS3
F: DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')
E: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)47,4016
Polymers47,4016
Non-polymers00
Water6,287349
1
A: B3 domain-containing transcription factor FUS3
C: DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')
B: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,7003
Polymers23,7003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-17 kcal/mol
Surface area10150 Å2
MethodPISA
2
D: B3 domain-containing transcription factor FUS3
F: DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')
E: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,7003
Polymers23,7003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-21 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.033, 95.033, 113.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein B3 domain-containing transcription factor FUS3 / Protein FUSCA3


Mass: 14523.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FUS3, At3g26790, MDJ14.4 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9LW31
#2: DNA chain DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)-3')


Mass: 4562.000 Da / Num. of mol.: 2 / Fragment: FLC CME DNA fragment / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)-3')


Mass: 4615.006 Da / Num. of mol.: 2 / Fragment: FLC CME DNA fragment / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M CaCl2, 0.1 M HEPES, pH 7.5, and 28% PEG400

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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: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 90833 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 21.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4577 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9A

6j9a


Resolution: 1.9→46.79 Å / Cross valid method: FREE R-VALUE / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.195 3967 4.37 %
Rwork0.176 --
obs0.181 90833 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 1214 0 349 3321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0263162
X-RAY DIFFRACTIONf_angle_d1.4864524
X-RAY DIFFRACTIONf_dihedral_angle_d30.8651254
X-RAY DIFFRACTIONf_chiral_restr0.145486
X-RAY DIFFRACTIONf_plane_restr0.01374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8984-1.93110.28992040.28644300X-RAY DIFFRACTION95
1.9311-1.96620.28661900.27994327X-RAY DIFFRACTION96
1.9662-2.0040.25532080.26644367X-RAY DIFFRACTION95
2.004-2.04490.27111940.2484295X-RAY DIFFRACTION96
2.0449-2.08940.27141920.24574388X-RAY DIFFRACTION96
2.0894-2.1380.25032040.25284297X-RAY DIFFRACTION95
2.138-2.19140.22691940.24094370X-RAY DIFFRACTION96
2.1914-2.25070.2451980.2354333X-RAY DIFFRACTION96
2.2507-2.31690.2642040.22944354X-RAY DIFFRACTION96
2.3169-2.39160.18151900.22874342X-RAY DIFFRACTION96
2.3916-2.47710.23982020.22374329X-RAY DIFFRACTION96
2.4771-2.57620.26761980.22644345X-RAY DIFFRACTION96
2.5762-2.69340.23962000.21264338X-RAY DIFFRACTION96
2.6934-2.83540.26551940.21084346X-RAY DIFFRACTION96
2.8354-3.01290.20751840.1964315X-RAY DIFFRACTION96
3.0129-3.24540.21462060.16674351X-RAY DIFFRACTION95
3.2454-3.57160.16052040.14214371X-RAY DIFFRACTION96
3.5716-4.08770.14692040.13824323X-RAY DIFFRACTION95
4.0877-5.1470.15312030.12724342X-RAY DIFFRACTION96
5.147-33.34560.20291940.15844337X-RAY DIFFRACTION96
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)
11.6108-0.31180.47422.8150.9072.97880.13490.01490.08920.0265-0.0062-0.17610.07290.0879-0.13050.1656-0.00490.04730.1617-0.00320.41312.7693-21.0083-36.5236
21.74471.553-1.87863.5002-2.26025.2087-0.04740.34930.4922-0.12210.29680.1258-0.4608-0.6011-0.19490.29850.02230.10690.30140.0250.49524.3013-8.937-38.1422
30.89050.6217-0.1091.6379-0.13082.07290.05660.02820.1115-0.1125-0.0189-0.0276-0.0222-0.0545-0.01730.17360.01750.05680.16710.01270.4099.6929-17.3057-38.3653
47.8019-3.55276.82172.5704-3.0818.3278-0.0769-1.1324-0.16480.16590.101-0.1428-0.0822-0.57650.02810.204-0.04180.0420.34350.0450.38264.7141-20.54285.1213
58.8374-4.9894-1.27784.0656-0.89262.23190.6068-0.596-0.19320.01030.0533-0.27180.4177-0.5591-0.65350.3152-0.0827-0.08230.51030.0320.484819.448-20.60479.4562
62.030.10443.50411.37421.14396.9976-0.0793-0.13930.37610.02960.1679-0.0363-0.39110.2935-0.07970.2265-0.0273-0.00130.313-0.01520.376520.2879-18.70693.178
79.3113-5.94640.9917.03422.56835.77170.2149-0.343-0.24940.1981-0.49380.11790.6843-0.3720.25390.271-0.0951-0.0160.21370.05050.3477.6159-27.0511-3.4359
86.6823-2.1838-0.47941.68610.56121.71550.21130.5635-0.0786-0.2659-0.0361-0.0799-0.0313-0.2323-0.15370.3086-0.0032-0.02280.26430.09240.40214.7303-21.732-12.1028
95.2583-1.3929-5.99584.04660.41388.69520.4641-0.43761.00230.17550.181-0.1841-0.92510.1956-0.5890.3142-0.01570.03760.2939-0.05850.55229.2497-7.73230.166
102.8942-0.0737-0.6812.83481.0212.53470.11130.010.44420.35110.0519-0.0605-0.02170.0979-0.17370.2218-0.04240.02030.21640.04250.40717.2553-17.9644-4.8045
112.8291-2.853-0.12096.76273.67356.96190.3502-0.0906-0.8267-0.02240.288-0.47330.586-0.2949-0.56860.252-0.0774-0.05990.26480.07990.640418.2337-26.7989-5.2548
121.04650.35171.10262.3023-0.12451.2913-0.0414-1.01620.75880.1799-0.41410.4063-0.45150.47140.29330.3536-0.18430.04540.4886-0.17970.603417.2172-9.64446.3091
134.2393-3.93311.52399.5182-3.52854.98150.2701-0.39140.0420.73980.1616-0.5601-0.40350.4382-0.33230.3652-0.0572-0.01060.4774-0.01650.398215.5705-16.584314.7664
143.4885-2.73663.51212.8869-3.77098.51280.07870.10210.01540.2317-0.1469-0.1289-0.52760.27360.01720.2081-0.03670.08710.2672-0.00460.36481.2922-14.0965-0.4215
152.58-0.55750.59132.7416-2.71625.79520.2247-0.92980.3560.5208-0.21640.019-0.33410.08680.00670.2441-0.08640.03150.47-0.07890.35866.8737-14.25878.8931
161.35930.1895-1.16761.076-0.78721.41920.0388-0.1174-0.0406-0.1258-0.0835-0.1710.14390.3634-0.02590.2048-0.0882-0.0710.29570.10040.597526.7349-29.45051.8609
171.48860.3732-0.52961.372-0.14141.69360.0254-0.3769-0.1024-0.29970.1128-0.06810.45570.2461-0.06540.3299-0.0726-0.0990.24080.13370.655428.6009-26.6145-0.6178
183.27030.3914-1.89561.3469-0.20242.1343-0.05070.3045-0.36140.04150.0074-0.05650.2-0.1521-0.00350.18510.00310.02280.2438-0.02820.558811.9508-36.5055-37.3222
193.52950.4545-0.74031.4915-0.11332.5063-0.1388-0.1769-0.3989-0.10180.0605-0.15910.2720.05560.01040.15970.02560.01780.2184-0.0250.52418.6542-36.6422-34.7278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'D' AND (RESID 89 THROUGH 126 )
2X-RAY DIFFRACTION2CHAIN 'D' AND (RESID 127 THROUGH 138 )
3X-RAY DIFFRACTION3CHAIN 'D' AND (RESID 139 THROUGH 194 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 89 THROUGH 95 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 96 THROUGH 101 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 102 THROUGH 110 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 111 THROUGH 117 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 118 THROUGH 126 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 127 THROUGH 138 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 139 THROUGH 149 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 150 THROUGH 158 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 159 THROUGH 167 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 168 THROUGH 173 )
14X-RAY DIFFRACTION14CHAIN 'A' AND (RESID 174 THROUGH 185 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 186 THROUGH 194 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 15 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 1 THROUGH 15 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 1 THROUGH 15 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 1 THROUGH 15 )

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