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- PDB-8xuf: CDF1 Dof domain in palindromic-bound complex with DNA duplex -

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Basic information

Entry
Database: PDB / ID: 8xuf
TitleCDF1 Dof domain in palindromic-bound complex with DNA duplex
Components
  • CDF1
  • DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')
  • DNA (5'-D(*TP*TP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')
KeywordsDNA/DNA BINDING PROTEIN / PLANT-SPECIFIC TRANSCRIPTION FACTOR / GENE SUPRESSION / CIS-ELEMENT / ZINC FINGER / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


regulation of timing of transition from vegetative to reproductive phase / vegetative to reproductive phase transition of meristem / chloroplast organization / flower development / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding ...regulation of timing of transition from vegetative to reproductive phase / vegetative to reproductive phase transition of meristem / chloroplast organization / flower development / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus
Similarity search - Function
Zinc finger, Dof-type / Dof zinc finger protein / Dof domain, zinc finger / Zinc finger Dof-type signature. / Zinc finger Dof-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Cyclic dof factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFurihata, H. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H04977 Japan
Japan Society for the Promotion of Science (JSPS)19H04855 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Agency for Medical Research and Development (AMED)24ama121010j0003 Japan
CitationJournal: Nat.Plants / Year: 2025
Title: Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain.
Authors: Furihata, H. / Zhu, Z. / Nishida, K. / Sakuraba, Y. / Tsuji, A. / Yamashita, H. / Nosaki, S. / Tachibana, R. / Yamagami, A. / Ikeda, Y. / Abe, M. / Sawasaki, T. / Nakano, T. / Yanagisawa, S. ...Authors: Furihata, H. / Zhu, Z. / Nishida, K. / Sakuraba, Y. / Tsuji, A. / Yamashita, H. / Nosaki, S. / Tachibana, R. / Yamagami, A. / Ikeda, Y. / Abe, M. / Sawasaki, T. / Nakano, T. / Yanagisawa, S. / Tanokura, M. / Miyakawa, T.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')
B: DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')
C: CDF1
D: CDF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2446
Polymers27,1134
Non-polymers1312
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Electrophoretic Mobility Shift Assay (EMSA)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.442, 79.442, 93.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 20)
d_2ens_1(chain "B" and resid 3 through 20)
d_1ens_2(chain "C" and (resid 50 through 64 or (resid 65...
d_2ens_2(chain "D" and (resid 50 through 51 or (resid 52...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1DCDCDGDGAA3 - 93 - 9
d_2ens_1DCDCDGDGBB3 - 93 - 9
d_1ens_2PROPROGLYGLYCC50 - 1006 - 56
d_2ens_2PROPROGLYGLYDD50 - 1006 - 56

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.2669655032, -0.963569646573, 0.0162159274666), (-0.963703212981, 0.266885823982, -0.00693355957703), (0.00235316638758, -0.0174783626225, -0.99984447263)-50.6456456318, -38.7955233178, -23.4658212637
2given(-0.30183417477, -0.953266697008, 0.0133691928077), (-0.952677983696, 0.302118961545, 0.0335975066872), (-0.0360664708752, -0.0025956599424, -0.999346022271)-51.1212454668, -38.3729253676, -24.0926609251

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Components

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


Mass: 6122.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')


Mass: 6140.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein CDF1 / Cyclic dof factor 1


Mass: 7425.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDF1, DOF5.5, At5g62430, K19B1.4, MMI9.24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W1E3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES-NaOH, 50 mM magnesium chloride hexahydrate and 30% polyethylene glycol (PEG) 550 monomethyl ether (MME)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→35.53 Å / Num. obs: 13900 / % possible obs: 99.79 % / Redundancy: 12.9 % / Biso Wilson estimate: 61.03 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05328 / Rpim(I) all: 0.01537 / Rrim(I) all: 0.0555 / Net I/σ(I): 34.42
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1344 / CC1/2: 0.821 / CC star: 0.95 / Rpim(I) all: 0.3817 / Rrim(I) all: 1.413 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.53 Å / SU ML: 0.3885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 693 4.99 %
Rwork0.2291 13191 -
obs0.2301 13884 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 814 2 36 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721741
X-RAY DIFFRACTIONf_angle_d1.00192529
X-RAY DIFFRACTIONf_chiral_restr0.0526271
X-RAY DIFFRACTIONf_plane_restr0.0116187
X-RAY DIFFRACTIONf_dihedral_angle_d28.3759693
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.868259490771
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.767934132495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.40381390.35452582X-RAY DIFFRACTION100
2.48-2.730.34721280.33662590X-RAY DIFFRACTION100
2.73-3.120.38591450.32512609X-RAY DIFFRACTION99.96
3.12-3.930.24071470.22412615X-RAY DIFFRACTION99.46
3.93-35.530.1921340.18162795X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: -31.3148184113 Å / Origin y: -11.1447246955 Å / Origin z: -11.5293060332 Å
111213212223313233
T0.607592855825 Å2-0.180889298508 Å2-0.0915463497235 Å2-0.713355644371 Å2-0.095520753863 Å2--0.661616179091 Å2
L1.06514236605 °20.233682505061 °23.44448103327 °2-0.100142595414 °22.09709034674 °2--4.6113942055 °2
S0.00175995583196 Å °-0.0323001814085 Å °-0.0678336449485 Å °-0.206026789981 Å °0.0453967631167 Å °0.271173852585 Å °0.070369945924 Å °-0.326526787992 Å °-0.00946023022163 Å °
Refinement TLS groupSelection details: all

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