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- PDB-7c9o: Crystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/... -

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Basic information

Entry
Database: PDB / ID: 7c9o
TitleCrystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/OsNF-YC2)
Components
  • (DNA (25-MER)) x 2
  • (Nuclear transcription factor Y subunit ...) x 2
  • Zinc finger protein HD1
KeywordsTRANSCRIPTION / photoperiodic flowering / CCT family / NF-CCT complex / specific DNA recognition
Function / homology
Function and homology information


positive regulation of short-day photoperiodism, flowering / positive regulation of unidimensional cell growth / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / short-day photoperiodism / CCAAT-binding factor complex / regulation of flower development / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding ...positive regulation of short-day photoperiodism, flowering / positive regulation of unidimensional cell growth / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / short-day photoperiodism / CCAAT-binding factor complex / regulation of flower development / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain ...CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear transcription factor Y subunit C-2 / Nuclear transcription factor Y subunit B-11 / Zinc finger protein HD1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Oryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsShen, C. / Liu, H. / Guan, Z. / Xing, Y. / Yin, P.
CitationJournal: Plant Cell / Year: 2020
Title: Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering.
Authors: Shen, C. / Liu, H. / Guan, Z. / Yan, J. / Zheng, T. / Yan, W. / Wu, C. / Zhang, Q. / Yin, P. / Xing, Y.
History
DepositionJun 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein HD1
B: Nuclear transcription factor Y subunit B-11
C: Nuclear transcription factor Y subunit C-2
D: DNA (25-MER)
E: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)46,1925
Polymers46,1925
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-84 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.080, 136.080, 62.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Nuclear transcription factor Y subunit ... , 2 types, 2 molecules BC

#2: Protein Nuclear transcription factor Y subunit B-11 / OsNF-YB11 / Protein DAYS TO HEADING 8 / Protein HEADING DATE 5 / Transcriptional activator HAP3H / OsHAP3H


Mass: 10849.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HD5, DTH8, GHD8, HAP3H, NFYB11, Os08g0174500, LOC_Os08g07740
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0J7P4
#3: Protein Nuclear transcription factor Y subunit C-2 / OsNF-YC2 / Transcriptional activator HAP5C / OsHAP5C


Mass: 11907.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: NFYC2, HAP5C, Os03g0251350, LOC_Os03g14669 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6BLW4

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA (25-MER)


Mass: 7531.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice)
#5: DNA chain DNA (25-MER)


Mass: 7825.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice)

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Protein / Non-polymers , 2 types, 17 molecules A

#1: Protein Zinc finger protein HD1 / Protein CONSTANS-like / Protein HEADING DATE 1 / OsHd1 / Protein PHOTOPERIOD SENSITIVITY 1


Mass: 8078.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HD1, SE1, Os06g0275000, LOC_Os06g16370, P0038C05.23, P0676F10.34
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FDX8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, sodium citrate, sodium acetate trihydrate, magnesium acetate tetrahydrate, glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.55→68.04 Å / Num. obs: 22041 / % possible obs: 99.5 % / Redundancy: 9.9 % / Biso Wilson estimate: 58.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 14.8
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2658 / CC1/2: 0.865 / Rpim(I) all: 0.267 / Rrim(I) all: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3206refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G92

4g92


Resolution: 2.55→43.02 Å / SU ML: 0.3051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6734
RfactorNum. reflection% reflection
Rfree0.2258 1063 4.84 %
Rwork0.1995 20920 -
obs0.2008 21983 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.53 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 1025 0 16 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972880
X-RAY DIFFRACTIONf_angle_d1.09364086
X-RAY DIFFRACTIONf_chiral_restr0.0551458
X-RAY DIFFRACTIONf_plane_restr0.0071346
X-RAY DIFFRACTIONf_dihedral_angle_d33.16831178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.670.29851420.29982576X-RAY DIFFRACTION98.94
2.67-2.810.32211400.27762575X-RAY DIFFRACTION98.91
2.81-2.980.33461060.28542606X-RAY DIFFRACTION98.55
2.98-3.210.30941290.27452573X-RAY DIFFRACTION98.83
3.21-3.540.27451200.21612627X-RAY DIFFRACTION99.31
3.54-4.050.18831350.19492623X-RAY DIFFRACTION99.78
4.05-5.10.19071520.15672623X-RAY DIFFRACTION99.78
5.1-43.020.191390.16382717X-RAY DIFFRACTION99.06
Refinement TLS params.Method: refined / Origin x: -57.3188911657 Å / Origin y: 10.9426816755 Å / Origin z: -4.46396780881 Å
111213212223313233
T0.697792996532 Å2-0.132507359836 Å2-0.022409493301 Å2-0.362097776509 Å20.0261952412828 Å2--0.364778032711 Å2
L1.79605684213 °22.18071478208 °2-0.499975420074 °2-4.96421601664 °2-0.676823742904 °2--1.17980102118 °2
S-0.255563256074 Å °0.255436570887 Å °-0.0645311608953 Å °-0.710141181552 Å °0.222144031449 Å °-0.384164695452 Å °-0.0528501448235 Å °0.167223582294 Å °0.0293527301337 Å °
Refinement TLS groupSelection details: all

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