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- PDB-7et4: Crystal structure of Arabidopsis TEM1 AP2 domain -

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Basic information

Entry
Database: PDB / ID: 7et4
TitleCrystal structure of Arabidopsis TEM1 AP2 domain
Components
  • (DNA (12-mer)) x 2
  • AP2/ERF and B3 domain-containing transcription repressor TEM1
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
A: AP2/ERF and B3 domain-containing transcription repressor TEM1
B: DNA (12-mer)
C: DNA (12-mer)
D: AP2/ERF and B3 domain-containing transcription repressor TEM1
E: DNA (12-mer)
F: DNA (12-mer)
G: AP2/ERF and B3 domain-containing transcription repressor TEM1
H: DNA (12-mer)
I: DNA (12-mer)
J: AP2/ERF and B3 domain-containing transcription repressor TEM1
K: DNA (12-mer)
L: DNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)84,75212
Polymers84,75212
Non-polymers00
Water2,504139
1
A: AP2/ERF and B3 domain-containing transcription repressor TEM1
B: DNA (12-mer)
C: DNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)21,1883
Polymers21,1883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-18 kcal/mol
Surface area9550 Å2
MethodPISA
2
D: AP2/ERF and B3 domain-containing transcription repressor TEM1
E: DNA (12-mer)
F: DNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)21,1883
Polymers21,1883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-21 kcal/mol
Surface area9670 Å2
MethodPISA
3
G: AP2/ERF and B3 domain-containing transcription repressor TEM1
H: DNA (12-mer)
I: DNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)21,1883
Polymers21,1883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-18 kcal/mol
Surface area9360 Å2
MethodPISA
4
J: AP2/ERF and B3 domain-containing transcription repressor TEM1
K: DNA (12-mer)
L: DNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)21,1883
Polymers21,1883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-20 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.316, 135.155, 66.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 13863.179 Da / Num. of mol.: 4 / Fragment: AP2 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
DNA (12-mer) / FT-GCC11-R


Mass: 3644.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain
DNA (12-mer) / FT-GCC11-F


Mass: 3680.432 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.85 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M NH4Cl, 0.1 M NaAc pH 5.0, 20% PEG 6000

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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 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27364 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.076 / Rrim(I) all: 0.16 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 2704 / CC1/2: 0.499 / CC star: 0.816 / Rpim(I) all: 0.464 / Rrim(I) all: 0.947 / % possible all: 100

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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: 1GCC

1gcc


Resolution: 2.7→35.524 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1392 5.1 %
Rwork0.2027 25921 -
obs0.2043 27313 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.99 Å2 / Biso mean: 55.0765 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: final / Resolution: 2.7→35.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 1881 0 139 5331
Biso mean---39.94 -
Num. residues----499
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.78560.35261400.3111233592
2.7856-2.89710.34071430.29412573100
2.8971-3.02880.29051230.26752592100
3.0288-3.18840.31191220.25582577100
3.1884-3.3880.21431420.19532589100
3.388-3.64940.24811330.2022594100
3.6494-4.01620.22141520.19022601100
4.0162-4.59630.1921410.16782621100
4.5963-5.78680.20591470.17372655100
5.7868-100.21211490.18672784100
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)
10.3978-0.10680.53460.2027-0.06180.82080.1141-0.3768-0.2275-0.06440.08940.10950.1806-0.20390.10540.13450.0251-0.03310.1857-0.03310.2485-37.3723-27.2621-59.3404
20.02860.0368-0.05040.1154-0.13730.1625-0.1382-0.12780.0398-0.05950.0299-0.1713-0.02430.0242-0.08120.1060.0652-0.03640.0984-0.11130.2813-31.0546-21.5204-63.6439
30.14570.088-0.00540.09610.00940.0048-0.1341-0.05380.20630.0615-0.1039-0.1632-0.18270.0167-0.18530.2224-0.0702-0.0990.2054-0.05960.5249-20.4231-20.0436-58.4612
40.00360.013-0.020.0447-0.05770.09970.02850.0896-0.0156-0.04060.0106-0.0174-0.0460.0408-0.00061.0380.0419-0.29561.0254-0.13541.175-13.3203-16.057-61.2022
50.0180.009-0.09210.0072-0.06170.4863-0.012-0.060.2446-0.11150.1683-0.0008-0.2254-0.11930.00940.1391-0.01330.03270.13790.02090.3338-27.6539-14.0079-70.8247
60.08730.0166-0.01260.0577-0.04720.09650.16250.2550.0755-0.10440.026-0.13380.15680.0910.00510.48910.00860.08940.40150.00450.398-19.7425-16.7211-78.3808
70.1143-0.0527-0.02680.0735-0.09880.28820.1823-0.4288-0.14690.0730.02990.16780.0928-0.30760.2675-0.1244-0.1396-0.30580.2671-0.14170.0126-46.791-23.4178-59.1504
80.3895-0.26090.06190.4229-0.110.0304-0.0032-0.32790.0690.13820.17950.3108-0.15720.0446-0.03340.2405-0.0467-0.07260.30610.01010.294-47.0295-23.4949-60.6706
90.21230.07710.11660.50010.49970.5458-0.0135-0.10280.02620.3010.126-0.07460.12220.16170.19170.1311-0.03990.1060.0757-0.03210.2729-29.890819.57785.1607
100.006-0.01420.00150.0527-0.02330.00860.12670.16480.24030.1744-0.13620.0912-0.0922-0.1167-0.00110.2723-0.0180.06340.2128-0.04680.3171-32.322235.88077.0929
110.1258-0.05710.02010.23560.09110.0466-0.10680.215-0.0663-0.1479-0.01820.3085-0.2144-0.0521-0.3224-0.2952-0.2794-0.01110.00920.04010.2264-37.371229.6071-7.4033
120.11330.05050.02410.09-0.05340.04950.11070.0422-0.13530.32570.04440.09890.1708-0.0420.00010.40880.00760.00180.2081-0.03260.319-30.83656.37886.002
130.48930.26790.33530.4627-0.0050.7350.2563-0.0242-0.24790.49610.2159-0.11520.1987-0.09850.51130.39960.02510.05040.2386-0.00260.3125-30.91046.63077.5328
140.0193-0.01210.01560.0175-0.01440.0127-0.0762-0.0275-0.20890.19160.01330.10610.0945-0.10880.00010.7285-0.2205-0.03050.5691-0.01310.462-26.2536-17.6051-29.6265
150.05020.04280.00170.0272-0.00990.04670.14130.12950.23590.3577-0.302-0.28180.0723-0.1542-0.00010.5384-0.0536-0.04510.4095-0.07230.5302-20.3607-7.475-32.9864
160.00740.01280.00590.00990.00690.00440.0611-0.09370.1521-0.0110.0038-0.1049-0.07760.1725-0.02780.7786-0.2302-0.37660.676-0.21380.8599-7.3375-6.3457-26.9208
170.0018-0.00330.01050.0208-0.05940.16710.07610.04560.0385-0.01430.0775-0.065-0.04220.03980.04210.6683-0.33350.0160.9390.19461.1883-5.2232-1.3858-38.7768
180.01670.01130.00630.0195-0.00530.01020.15110.0980.2015-0.13860.1051-0.0315-0.08410.03070.0010.578-0.02430.00080.47020.08650.6079-17.1932-2.2291-42.2461
190.00910.00450.00680.02820.03180.0344-0.07050.13340.0115-0.0148-0.16590.0281-0.0352-0.0942-0.00010.49390.00190.03070.50030.14460.5435-9.202-8.6838-46.3852
200.1256-0.0296-0.18320.0652-0.12740.6340.5673-0.0448-0.01280.2287-0.3572-0.1304-0.1177-0.58550.06470.7176-0.1173-0.00360.5264-0.1550.3924-34.5137-7.1883-29.6374
210.2939-0.12-0.27790.03490.11020.26040.20890.05670.29350.436-0.1929-0.0065-0.0605-0.36860.1370.7744-0.12610.02210.4911-0.20540.4028-33.6264-7.0965-27.5214
220.0365-0.0026-0.00370.1298-0.01380.0339-0.1212-0.32030.00530.06120.04550.04760.23740.0509-0.00040.5471-0.01740.14610.5849-0.06110.5341-42.535528.009335.2643
230.00640.0096-0.00160.0443-0.02530.0263-0.0479-0.13420.1545-0.07240.22370.0252-0.1766-0.23590.00310.59420.06430.0260.7002-0.07350.6775-47.027239.160635.7452
240.0145-0.01080.00450.0355-0.02610.0240.06710.3230.0248-0.17950.16740.36850.0227-0.179-0.00040.47280.0485-0.14850.7833-0.05510.7725-47.582847.02932.7176
250.0163-0.00420.0020.0014-0.00120.0103-0.02130.2954-0.1209-0.3372-0.2690.04990.1052-0.0215-0.00060.8032-0.0561-0.09110.75490.0390.4781-46.433841.643922.273
260.05930.05720.07820.02820.05510.068-0.332-0.1533-0.16270.01170.35110.08590.6182-0.33290.00020.6551-0.03210.20750.7137-0.03750.4392-46.952718.728837.0632
270.08550.0270.06690.0457-0.00110.0608-0.4397-0.3385-0.03270.00070.44810.1280.24270.06210.01570.63830.00420.18240.6787-0.05480.4589-47.134420.37840.0244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 91 )A65 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 117 )A92 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 127 )A118 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 133 )A128 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 155 )A134 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 166 )A156 - 166
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 12 )B1 - 12
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )C1 - 11
9X-RAY DIFFRACTION9chain 'D' and (resid 66 through 117 )D66 - 117
10X-RAY DIFFRACTION10chain 'D' and (resid 118 through 132 )D118 - 132
11X-RAY DIFFRACTION11chain 'D' and (resid 133 through 169 )D133 - 169
12X-RAY DIFFRACTION12chain 'E' and (resid 7 through 17 )E7 - 17
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 12 )F1 - 12
14X-RAY DIFFRACTION14chain 'G' and (resid 66 through 82 )G66 - 82
15X-RAY DIFFRACTION15chain 'G' and (resid 83 through 117 )G83 - 117
16X-RAY DIFFRACTION16chain 'G' and (resid 118 through 132 )G118 - 132
17X-RAY DIFFRACTION17chain 'G' and (resid 133 through 141 )G133 - 141
18X-RAY DIFFRACTION18chain 'G' and (resid 142 through 152 )G142 - 152
19X-RAY DIFFRACTION19chain 'G' and (resid 153 through 164 )G153 - 164
20X-RAY DIFFRACTION20chain 'H' and (resid 1 through 12 )H1 - 12
21X-RAY DIFFRACTION21chain 'I' and (resid 1 through 11 )I1 - 11
22X-RAY DIFFRACTION22chain 'J' and (resid 67 through 101 )J67 - 101
23X-RAY DIFFRACTION23chain 'J' and (resid 102 through 122 )J102 - 122
24X-RAY DIFFRACTION24chain 'J' and (resid 123 through 143 )J123 - 143
25X-RAY DIFFRACTION25chain 'J' and (resid 144 through 167 )J144 - 167
26X-RAY DIFFRACTION26chain 'K' and (resid 1 through 12 )K1 - 12
27X-RAY DIFFRACTION27chain 'L' and (resid 1 through 12 )L1 - 12

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