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- PDB-7vp7: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp7
TitleStructure of a transcription factor and DNA complex
Components
  • (DNA (5'-D(P*AP*GP*GP*CP*CP*CP*CP*CP*CP*CP*AP*T)-3')) x 2
  • Transcription factor TCP10
KeywordsDNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


leaf senescence / leaf development / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / 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 TCP10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 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 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

Downloads & links

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Assembly

Deposited unit
A: Transcription factor TCP10
B: Transcription factor TCP10
C: DNA (5'-D(P*AP*GP*GP*CP*CP*CP*CP*CP*CP*CP*AP*T)-3')
D: DNA (5'-D(P*AP*GP*GP*CP*CP*CP*CP*CP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)34,1654
Polymers34,1654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-36 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.756, 78.756, 82.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcription factor TCP10


Mass: 11886.519 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TCP10, At2g31070, T16B12.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O82277
#2: DNA chain DNA (5'-D(P*AP*GP*GP*CP*CP*CP*CP*CP*CP*CP*AP*T)-3')


Mass: 5117.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*GP*CP*CP*CP*CP*CP*CP*CP*AP*T)-3')


Mass: 5274.405 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH 8.0 and 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.653→35.562 Å / Num. obs: 8931 / % possible obs: 96.4 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.61
Reflection shellResolution: 2.653→2.748 Å / Rmerge(I) obs: 0.7905 / Num. unique obs: 586

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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: 2.653→35.562 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 806 -
Rwork0.2057 10848 -
obs-8616 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.39 Å2 / Biso mean: 41.0638 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 2.653→35.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 490 0 0 1323
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011420
X-RAY DIFFRACTIONf_angle_d1.0612017
X-RAY DIFFRACTIONf_chiral_restr0.056225
X-RAY DIFFRACTIONf_plane_restr0.006168
X-RAY DIFFRACTIONf_dihedral_angle_d20.324766
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.653-2.75890.3282640.323261637
2.7589-2.88440.4215930.313784851
2.8844-3.03640.30141000.282290154
3.0364-3.22660.3071070.269495358
3.2266-3.47550.30651300.2052113968
3.4755-3.82490.24231610.1896140685
3.8249-4.37750.24341830.1629168199
4.3775-5.51190.22981850.17931644100
5.5119-35.5620.211870.19991660100
Refinement TLS params.Method: refined / Origin x: 30.2974 Å / Origin y: -21.98 Å / Origin z: 33.6245 Å
111213212223313233
T0.1405 Å2-0.0741 Å2-0.0591 Å2--0.0597 Å2-0.0059 Å2--0.0819 Å2
L0.4189 °20.0669 °20.1255 °2-0.2808 °20.1543 °2--0.158 °2
S-0.0408 Å °0.0059 Å °0.153 Å °-0.0473 Å °0.0026 Å °0.0093 Å °-0.0419 Å °0.0083 Å °-0.1215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 87
2X-RAY DIFFRACTION1allB43 - 87
3X-RAY DIFFRACTION1allC5 - 15
4X-RAY DIFFRACTION1allD1 - 13

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