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- PDB-7et6: Crystal structure of Arabidopsis TEM1 B3-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7et6
TitleCrystal structure of Arabidopsis TEM1 B3-DNA complex
Components
  • AP2/ERF and B3 domain-containing transcription repressor TEM1
  • FT-RY14-F
  • FT-RY14-R
KeywordsDNA BINDING PROTEIN/DNA / GENE REGULATION / Flowering time regulation / plant protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


photoperiodism, flowering / ethylene-activated signaling pathway / cellular response to hypoxia / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
B3 domain-containing transcription factor LEC2-like / AP2/ERF domain superfamily / AP2/ERF domain profile. / DNA-binding domain in plant proteins such as APETALA2 and EREBPs / AP2/ERF domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / AP2/ERF and B3 domain-containing transcription repressor TEM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHu, H. / Du, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis.
Authors: Hu, H. / Tian, S. / Xie, G. / Liu, R. / Wang, N. / Li, S. / He, Y. / Du, J.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: AP2/ERF and B3 domain-containing transcription repressor TEM1
A: AP2/ERF and B3 domain-containing transcription repressor TEM1
E: FT-RY14-F
F: FT-RY14-R


Theoretical massNumber of molelcules
Total (without water)37,9834
Polymers37,9834
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-35 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.760, 68.760, 162.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein AP2/ERF and B3 domain-containing transcription repressor TEM1 / Protein TEMPRANILLO 1 / RAV1-like ethylene-responsive transcription factor TEM1


Mass: 14402.643 Da / Num. of mol.: 2 / Fragment: B3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TEM1, At1g25560, F2J7.3 / Plasmid: psumo / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): Rosseta / References: UniProt: Q9C6M5
#2: DNA chain FT-RY14-F


Mass: 4568.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain FT-RY14-R


Mass: 4609.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MgAc, 0.1 M MES pH 6.5, 10% PEG 10000

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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 S 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12666 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Net I/σ(I): 18.6
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1227 / CC1/2: 0.513 / CC star: 0.824 / Rpim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDW

4ldw


Resolution: 2.7→36.231 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 518 4.96 %
Rwork0.232 9919 -
obs0.2338 10437 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.86 Å2 / Biso mean: 63.2222 Å2 / Biso min: 22.49 Å2
Refinement stepCycle: final / Resolution: 2.7→36.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 609 0 23 2389
Biso mean---44.91 -
Num. residues----241
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.97120.3799910.3229179569
2.9712-3.40090.28471270.2579264299
3.4009-4.28370.26171310.222684100
4.2837-100.24711690.2172279899
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)
12.32420.37780.10323.9382.19843.5340.09781.3587-0.8188-1.4601-0.06150.52090.7453-0.8861-0.00371.047-0.088-0.22041.2283-0.25920.529216.16889.6252-56.2092
25.45940.1992-3.6895.25381.02714.43440.25540.0920.5226-0.21460.08090.0853-0.3721-0.2256-0.37520.26550.06310.00230.1974-0.05160.360720.699822.2391-40.5853
32.96430.38332.02692.16640.34981.3890.13541.43110.22-1.4075-0.09931.3254-0.0594-1.1971-0.00620.58610.1279-0.31730.95040.09540.57319.274619.13-49.4837
40.163-0.19470.15524.4819-2.37061.98840.06190.28730.3252-0.29840.33031.0450.2653-0.6344-0.37820.66340.3211-0.1762.1863-0.35070.91433.269611.3015-44.8635
56.40463.00180.16637.2215-1.6778.6023-0.24830.7088-1.1745-0.8065-0.0483-0.31221.64950.12720.30590.58950.01470.02470.5937-0.24920.540418.21143.7699-45.0111
67.33770.1608-0.46442.1569-0.38277.0666-0.0105-0.0446-0.16040.0235-0.13131.08610.3391-0.86540.11610.2859-0.0971-0.09380.5057-0.17060.429212.188311.7013-39.8327
75.85962.4498-0.41146.7051-0.94387.6114-0.05590.10370.3082-0.0416-0.1910.1794-0.22020.24920.23710.24990.0501-0.0120.54470.02740.102319.245416.4672-41.351
80.4639-1.04070.42732.61680.38076.82590.26780.3556-0.4665-0.1428-0.50460.77411.4223-0.87020.14940.7764-0.0385-0.15511.3726-0.53380.69313.3153.9151-52.9363
91.4253-1.141-0.19741.96611.44148.94690.1590.433-0.2363-0.3643-0.0938-0.15290.2150.73130.01620.44550.2268-0.08631.3304-0.38470.518924.451512.3054-51.8338
100.28720.0717-0.08624.80711.0014.0688-0.0286-0.5117-0.87550.68020.0274-1.14850.90860.3886-0.00690.67130.146-0.01990.43960.20450.774720.3718.2813-2.7658
115.49142.19820.42916.48294.16424.3321-0.18120.1315-0.5299-1.02270.0591-0.50750.18430.22540.10110.60460.07140.18660.2297-0.06440.380916.247925.8102-15.4196
121.7176-0.00020.45416.98911.79240.8151-0.0105-0.2857-1.02060.54340.1065-0.76460.89350.287-0.05120.80430.19720.24610.31970.11180.886217.719911.463-7.2691
135.5126-0.49831.84755.01251.61324.8307-0.25440.3316-2.14680.72790.3690.00721.83910.2863-0.10091.07040.12560.28970.5606-0.04641.23556.40258.1736-10.2801
142.29932.44441.11493.50661.06712.5643-0.221-0.526-0.79151.21640.457-0.19010.35870.0857-0.24170.84580.25050.11460.55880.07250.54445.993822.43120.4188
155.0573-2.9944-0.18057.1355.12095.4272-0.06850.3069-0.87410.3053-0.4240.40430.5482-0.30270.53750.740.07380.3560.35930.04850.56436.891917.4519-9.8117
163.8324-1.11730.99383.54013.07494.29440.18870.7673-0.9495-0.1165-0.2688-0.02440.42870.21720.03060.82150.17360.32520.3622-0.08120.634711.55714.1149-15.6134
174.2954.5015-0.96949.81220.48347.1096-0.2958-0.12040.36510.66540.34890.9893-0.1575-0.4773-0.07750.45530.06780.12090.25560.08780.39729.568529.706-7.7661
185.09865.2622-1.19277.9146-2.88434.47210.0499-0.7728-1.02171.0329-0.2563-0.6650.19620.27430.24220.71770.2719-0.01220.35020.1170.509917.565724.9172-2.8571
193.98620.89260.88893.5173-2.6334.63630.2796-1.2277-1.14330.8283-0.2485-0.21290.14270.08170.0181.5220.3956-0.05850.82050.27870.623613.095820.46734.0263
204.2818-1.9076-0.73312.64990.66861.9754-0.06170.556-0.23230.5888-0.10870.20750.02130.14090.14420.43390.2415-0.01260.4098-0.01580.774514.678419.9316-22.7165
210.2097-0.0124-0.25220.2220.12410.3668-0.08420.0214-0.27820.1026-0.07150.00480.22760.0470.08990.30820.61250.0250.4838-0.31720.910715.970516.6408-23.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 189 through 198 )D189 - 198
2X-RAY DIFFRACTION2chain 'D' and (resid 199 through 209 )D199 - 209
3X-RAY DIFFRACTION3chain 'D' and (resid 210 through 218 )D210 - 218
4X-RAY DIFFRACTION4chain 'D' and (resid 219 through 239 )D219 - 239
5X-RAY DIFFRACTION5chain 'D' and (resid 240 through 250 )D240 - 250
6X-RAY DIFFRACTION6chain 'D' and (resid 251 through 259 )D251 - 259
7X-RAY DIFFRACTION7chain 'D' and (resid 260 through 284 )D260 - 284
8X-RAY DIFFRACTION8chain 'D' and (resid 285 through 297 )D285 - 297
9X-RAY DIFFRACTION9chain 'D' and (resid 298 through 307 )D298 - 307
10X-RAY DIFFRACTION10chain 'A' and (resid 194 through 198 )A194 - 198
11X-RAY DIFFRACTION11chain 'A' and (resid 199 through 209 )A199 - 209
12X-RAY DIFFRACTION12chain 'A' and (resid 210 through 220 )A210 - 220
13X-RAY DIFFRACTION13chain 'A' and (resid 221 through 239 )A221 - 239
14X-RAY DIFFRACTION14chain 'A' and (resid 240 through 250 )A240 - 250
15X-RAY DIFFRACTION15chain 'A' and (resid 251 through 259 )A251 - 259
16X-RAY DIFFRACTION16chain 'A' and (resid 260 through 270 )A260 - 270
17X-RAY DIFFRACTION17chain 'A' and (resid 271 through 278 )A271 - 278
18X-RAY DIFFRACTION18chain 'A' and (resid 279 through 290 )A279 - 290
19X-RAY DIFFRACTION19chain 'A' and (resid 291 through 306 )A291 - 306
20X-RAY DIFFRACTION20chain 'E' and (resid 1 through 15 )E1 - 15
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 15 )F1 - 15

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