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- PDB-7vp5: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp5
TitleStructure of a transcription factor and DNA complex
Components
  • (DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*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: 2.992 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(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
D: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
E: Transcription factor TCP10
F: Transcription factor TCP10
G: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
H: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
I: Transcription factor TCP10
J: Transcription factor TCP10
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
L: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')


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


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-53 kcal/mol
Surface area10540 Å2
MethodPISA
2
E: Transcription factor TCP10
F: Transcription factor TCP10
G: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
H: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-54 kcal/mol
Surface area10190 Å2
MethodPISA
3
I: Transcription factor TCP10
J: Transcription factor TCP10
K: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')
L: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-47 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.766, 76.896, 83.078
Angle α, β, γ (deg.)90.000, 113.850, 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*GP*TP*GP*T)-3')


Mass: 4302.788 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')


Mass: 4258.795 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: 2.32 Å3/Da / Density % sol: 46.95 %
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: 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: 2.992→29.1 Å / Num. obs: 18354 / % possible obs: 97.76 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.1649 / Net I/σ(I): 8.8
Reflection shellResolution: 2.992→3.098 Å / Rmerge(I) obs: 0.7659 / Num. unique obs: 1508

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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: 2.992→29.1 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1783 -
Rwork0.2092 16146 -
obs-17928 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.5 Å2 / Biso mean: 59.0469 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.992→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 1704 0 0 4487
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094761
X-RAY DIFFRACTIONf_angle_d1.0046804
X-RAY DIFFRACTIONf_chiral_restr0.051770
X-RAY DIFFRACTIONf_plane_restr0.006586
X-RAY DIFFRACTIONf_dihedral_angle_d20.112528
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.992-3.06930.4031070.299790270
3.0693-3.15950.31461320.2405121094
3.1595-3.26140.29661410.2208122398
3.2614-3.37780.28421370.2148125199
3.3778-3.51280.31961410.2323125699
3.5128-3.67240.33461430.21881283100
3.6724-3.86560.28251510.22541267100
3.8656-4.10710.28631460.19661270100
4.1071-4.42320.24321370.17151290100
4.4232-4.86650.24351350.17631291100
4.8665-5.56640.25671390.19091294100
5.5664-6.9970.231360.2002129399
6.997-29.10.20781380.188131699
Refinement TLS params.Method: refined / Origin x: 94.5111 Å / Origin y: -7.492 Å / Origin z: 91.4542 Å
111213212223313233
T0.3 Å20.0569 Å2-0.011 Å2-0.2508 Å2-0.0369 Å2--0.3356 Å2
L0.7176 °20.4271 °20.0218 °2-0.7461 °2-0.3513 °2--0.9479 °2
S-0.0276 Å °-0.1557 Å °0.0966 Å °-0.0076 Å °0.0211 Å °-0.0434 Å °0.0555 Å °-0.0162 Å °0.0213 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 87
2X-RAY DIFFRACTION1allB14 - 86
3X-RAY DIFFRACTION1allC1 - 14
4X-RAY DIFFRACTION1allD1 - 14
5X-RAY DIFFRACTION1allE32 - 87
6X-RAY DIFFRACTION1allF14 - 87
7X-RAY DIFFRACTION1allG1 - 14
8X-RAY DIFFRACTION1allH1 - 14
9X-RAY DIFFRACTION1allI33 - 87
10X-RAY DIFFRACTION1allJ30 - 85
11X-RAY DIFFRACTION1allK1 - 14
12X-RAY DIFFRACTION1allL1 - 14

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