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- PDB-7vp3: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp3
TitleStructure of a transcription factor and DNA complex
Components
  • DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
  • Transcription factor TCP15
KeywordsDNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division ...stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor, TCP / Transcription factor TCP subgroup / TCP family transcription factor / TCP domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor TCP15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsZhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670740 China
National Science Foundation (NSF, China)31270803 China
CitationJournal: To Be Published
Title: Structural basis for DNA recognition by TCP transcription factors
Authors: Zhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 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
B: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
D: Transcription factor TCP15
E: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
J: Transcription factor TCP15
A: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
C: Transcription factor TCP15
F: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
G: Transcription factor TCP15
H: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
I: Transcription factor TCP15
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
L: Transcription factor TCP15
M: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
O: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
N: Transcription factor TCP15
P: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)94,58216
Polymers94,58216
Non-polymers00
Water00
1
B: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
D: Transcription factor TCP15
E: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
J: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)23,6454
Polymers23,6454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-62 kcal/mol
Surface area8640 Å2
MethodPISA
2
A: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
C: Transcription factor TCP15
F: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
G: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)23,6454
Polymers23,6454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-62 kcal/mol
Surface area8100 Å2
MethodPISA
3
H: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
I: Transcription factor TCP15
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
L: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)23,6454
Polymers23,6454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-63 kcal/mol
Surface area8600 Å2
MethodPISA
4
M: DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')
O: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')
N: Transcription factor TCP15
P: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)23,6454
Polymers23,6454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-61 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.219, 112.784, 156.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain
DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3')


Mass: 3672.406 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Transcription factor TCP15 / AtTCP15


Mass: 8159.337 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TCP15, At1g69690, T6C23.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9C9L2
#3: DNA chain
DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3')


Mass: 3654.378 Da / Num. of mol.: 4 / 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: 3.33 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium citrate/Citric acid pH 5.5, 20% w/v PEG 4000 and 10% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.003→18.17 Å / Num. obs: 25799 / % possible obs: 93.27 % / Redundancy: 25.9 % / Rmerge(I) obs: 0.2602 / Rrim(I) all: 0.2654 / Net I/σ(I): 19.26
Reflection shellResolution: 3.003→3.11 Å / Rmerge(I) obs: 0.8339 / Num. unique obs: 1836

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VP2

7vp2


Resolution: 3.003→18.17 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1210 -
Rwork0.1978 22989 -
obs-24198 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.52 Å2 / Biso mean: 60.8407 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.003→18.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 1825 0 0 5399
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015685
X-RAY DIFFRACTIONf_angle_d1.1658060
X-RAY DIFFRACTIONf_chiral_restr0.059920
X-RAY DIFFRACTIONf_plane_restr0.006733
X-RAY DIFFRACTIONf_dihedral_angle_d16.2183081
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0032-3.12290.40121310.3193191672
3.1229-3.26430.26871180.2507220582
3.2643-3.43530.25971160.2158246491
3.4353-3.64890.24521370.2019263098
3.6489-3.92810.26031420.21432701100
3.9281-4.31870.2381400.17042699100
4.3187-4.93280.22951450.15682740100
4.9328-6.17480.23911400.1662747100
6.1748-18.170.21111410.16392887100
Refinement TLS params.Method: refined / Origin x: 9.3478 Å / Origin y: -22.94 Å / Origin z: -38.741 Å
111213212223313233
T0.4223 Å20.0245 Å20.006 Å2-0.4649 Å2-0.0076 Å2--0.4893 Å2
L-0.2228 °2-0.0067 °20.1234 °2-0.1085 °20.0911 °2--0.8854 °2
S-0.0851 Å °-0.0006 Å °-0.0314 Å °-0.0028 Å °0.0439 Å °-0.0509 Å °0.0573 Å °0.1182 Å °0.0462 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 11
2X-RAY DIFFRACTION1allD51 - 108
3X-RAY DIFFRACTION1allE1 - 12
4X-RAY DIFFRACTION1allJ52 - 109
5X-RAY DIFFRACTION1allA1 - 11
6X-RAY DIFFRACTION1allC52 - 113
7X-RAY DIFFRACTION1allF2 - 12
8X-RAY DIFFRACTION1allG51 - 106
9X-RAY DIFFRACTION1allH1 - 11
10X-RAY DIFFRACTION1allI51 - 109
11X-RAY DIFFRACTION1allK1 - 12
12X-RAY DIFFRACTION1allL51 - 109
13X-RAY DIFFRACTION1allM1 - 12
14X-RAY DIFFRACTION1allO2 - 11
15X-RAY DIFFRACTION1allN52 - 113
16X-RAY DIFFRACTION1allP51 - 111

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