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- PDB-7vp4: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp4
TitleStructure of a transcription factor and DNA complex
Components
  • DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
  • DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')
  • 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: 3.04 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

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Assembly

Deposited unit
B: Transcription factor TCP10
A: Transcription factor TCP10
C: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
D: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')
F: Transcription factor TCP10
E: Transcription factor TCP10
G: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
H: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')
J: Transcription factor TCP10
I: Transcription factor TCP10
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
L: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)97,00412
Polymers97,00412
Non-polymers00
Water00
1
B: Transcription factor TCP10
A: Transcription factor TCP10
C: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
D: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-53 kcal/mol
Surface area10600 Å2
MethodPISA
2
F: Transcription factor TCP10
E: Transcription factor TCP10
G: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
H: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-49 kcal/mol
Surface area10640 Å2
MethodPISA
3
J: Transcription factor TCP10
I: Transcription factor TCP10
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')
L: DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-55 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.603, 76.930, 83.227
Angle α, β, γ (deg.)90.000, 113.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcription factor TCP10


Mass: 11886.519 Da / Num. of mol.: 6
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(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*GP*T)-3')


Mass: 4271.777 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Mass: 4289.805 Da / Num. of mol.: 3 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium HEPES pH 7.0, 10% 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: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.04→29.16 Å / Num. obs: 17509 / % possible obs: 97.13 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1001 / Net I/σ(I): 14.46
Reflection shellResolution: 3.04→3.149 Å / Rmerge(I) obs: 0.4615 / Num. unique obs: 1650

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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: 7VP3

7vp3


Resolution: 3.04→29.16 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1732 -
Rwork0.2113 15448 -
obs-17178 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.32 Å2 / Biso mean: 67.3689 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.04→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 1704 0 0 4779
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015107
X-RAY DIFFRACTIONf_angle_d1.0867228
X-RAY DIFFRACTIONf_chiral_restr0.055806
X-RAY DIFFRACTIONf_plane_restr0.006629
X-RAY DIFFRACTIONf_dihedral_angle_d21.0542779
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.04-3.12920.34251230.232111485
3.1292-3.23010.29151420.2152125594
3.2301-3.34540.34111390.2269128898
3.3454-3.47910.31731450.2235126297
3.4791-3.63720.3171540.2245130999
3.6372-3.82850.31111360.2165130199
3.8285-4.06780.2811480.2027131999
4.0678-4.38090.22851480.1712131299
4.3809-4.820.23511470.1558129399
4.82-5.51340.23261460.16721333100
5.5134-6.93090.24111510.1962132199
6.9309-29.160.22161530.1869134198
Refinement TLS params.Method: refined / Origin x: 76.3114 Å / Origin y: -7.4791 Å / Origin z: 130.8704 Å
111213212223313233
T0.3477 Å20.019 Å2-0.0127 Å2-0.3257 Å2-0.0285 Å2--0.3695 Å2
L0.5884 °20.2525 °2-0.0821 °2-0.533 °2-0.2377 °2--0.7129 °2
S-0.0406 Å °-0.1619 Å °0.0768 Å °-0.0015 Å °0.0561 Å °-0.0437 Å °0.0296 Å °-0.0358 Å °-0.015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB21 - 84
2X-RAY DIFFRACTION1allA14 - 87
3X-RAY DIFFRACTION1allC1 - 14
4X-RAY DIFFRACTION1allD1 - 14
5X-RAY DIFFRACTION1allF30 - 83
6X-RAY DIFFRACTION1allE13 - 87
7X-RAY DIFFRACTION1allG1 - 14
8X-RAY DIFFRACTION1allH1 - 14
9X-RAY DIFFRACTION1allJ17 - 87
10X-RAY DIFFRACTION1allI32 - 87
11X-RAY DIFFRACTION1allK1 - 14
12X-RAY DIFFRACTION1allL1 - 14

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