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- PDB-7fdo: Crystal structure of transcription factor CPC in complex with EGL3 -

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Basic information

Entry
Database: PDB / ID: 7fdo
TitleCrystal structure of transcription factor CPC in complex with EGL3
Components
  • Transcription factor CPC
  • Transcription factor EGL1
KeywordsTRANSCRIPTION / Transcription factor complex
Function / homology
Function and homology information


positive regulation of trichoblast fate specification / trichome differentiation / stomatal complex formation / jasmonic acid mediated signaling pathway / epidermal cell fate specification / epidermal cell differentiation / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
: / : / Plant bHLH transcription factor, ACT-like domain / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain ...: / : / Plant bHLH transcription factor, ACT-like domain / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transcription factor CPC / Transcription factor EGL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsWang, B. / Luo, Q.
CitationJournal: Nat.Plants / Year: 2021
Title: Structural insights into partner selection for MYB and bHLH transcription factor complexes.
Authors: Wang, B. / Luo, Q. / Li, Y. / Du, K. / Wu, Z. / Li, T. / Shen, W.H. / Huang, C.H. / Gan, J. / Dong, A.
History
DepositionJul 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor EGL1
B: Transcription factor CPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0694
Polymers28,9382
Non-polymers1322
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-27 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.054, 50.358, 81.657
Angle α, β, γ (deg.)90.000, 97.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription factor EGL1 / Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / ...Basic helix-loop-helix protein 2 / AtMYC146 / AtbHLH2 / bHLH 2 / Protein ENHANCER OF GLABRA 3 / Transcription factor EN 30 / bHLH transcription factor bHLH002


Mass: 21682.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BHLH2, EGL1, EGL3, EN30, MYC146, At1g63650, F24D7.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CAD0
#2: Protein Transcription factor CPC / Protein CAPRICE


Mass: 7255.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CPC, At2g46410, F11C10.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O22059
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 6.5, 20% PEG3350, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 34121 / % possible obs: 97.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.01 / Rrim(I) all: 0.026 / Χ2: 0.914 / Net I/σ(I): 20.9 / Num. measured all: 209244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.815.20.31334380.2750.1470.3480.98398.9
1.81-1.895.70.18234230.9830.0820.20.76198.8
1.89-1.975.90.1434330.9910.0610.1530.86598.7
1.97-2.0760.10234240.9960.0450.1120.92498.1
2.07-2.260.05634020.9980.0240.0610.92698
2.2-2.376.70.04334890.9990.0180.0460.96599.8
2.37-2.616.70.03334780.9990.0130.0350.9599.4
2.61-2.996.50.02633930.9990.0110.0280.95497.2
2.99-3.776.60.02133940.9990.0090.0230.99796.4
3.77-306.20.01832470.9990.0080.020.78690.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC7.0.076refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RRU

4rru


Resolution: 1.752→28.701 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 1679 5.15 %
Rwork0.1981 --
obs0.1993 32622 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.64 Å2 / Biso mean: 31.0383 Å2 / Biso min: 5.94 Å2
Refinement stepCycle: final / Resolution: 1.752→28.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 6 139 1840
Biso mean--57.6 33.42 -
Num. residues----214
LS refinement shellResolution: 1.752→1.8036 Å
RfactorNum. reflection
Rfree0.2486 104
Rwork0.2186 -
obs-1974

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