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- PDB-3axy: Structure of Florigen Activation Complex Consisting of Rice Flori... -

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Basic information

Entry
Database: PDB / ID: 3axy
TitleStructure of Florigen Activation Complex Consisting of Rice Florigen Hd3a, 14-3-3 Protein GF14 and Rice FD Homolog OsFD1
Components
  • 14-3-3-like protein GF14-C
  • Protein HEADING DATE 3A
  • Rice FD homolog OsFD1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / Phosphatidylethanolamine-binding Protein / 14-3-3 Protein / bZip protein / Floral Induction / Transcriptional Activator / Signaling Protein / DNA Binding / Phosphorylation / Nucleus / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


short-day photoperiodism, flowering / short-day photoperiodism / regulation of timing of transition from vegetative to reproductive phase / inflorescence development / regulation of flower development / vegetative to reproductive phase transition of meristem / flower development / phosphatidylethanolamine binding / cell differentiation / nucleus / cytoplasm
Similarity search - Function
Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / 14-3-3 domain / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Delta-Endotoxin; domain 1 ...Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / 14-3-3 domain / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
14-3-3-like protein GF14-C / Protein HEADING DATE 3A
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOhki, I. / Furuita, K. / Hayashi, K. / Taoka, K. / Tsuji, H. / Nakagawa, A. / Shimamoto, K. / Kojima, C.
CitationJournal: Nature / Year: 2011
Title: 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen
Authors: Taoka, K. / Ohki, I. / Tsuji, H. / Furuita, K. / Hayashi, K. / Yanase, T. / Yamaguchi, M. / Nakashima, C. / Purwestri, Y.A. / Tamaki, S. / Ogaki, Y. / Shimada, C. / Nakagawa, A. / Kojima, C. / Shimamoto, K.
History
DepositionApr 19, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein HEADING DATE 3A
B: Protein HEADING DATE 3A
C: 14-3-3-like protein GF14-C
D: 14-3-3-like protein GF14-C
E: Rice FD homolog OsFD1
F: Rice FD homolog OsFD1
G: Protein HEADING DATE 3A
H: Protein HEADING DATE 3A
I: 14-3-3-like protein GF14-C
J: 14-3-3-like protein GF14-C
K: Rice FD homolog OsFD1
L: Rice FD homolog OsFD1


Theoretical massNumber of molelcules
Total (without water)188,98212
Polymers188,98212
Non-polymers00
Water13,998777
1
A: Protein HEADING DATE 3A
B: Protein HEADING DATE 3A
C: 14-3-3-like protein GF14-C
D: 14-3-3-like protein GF14-C
E: Rice FD homolog OsFD1
F: Rice FD homolog OsFD1


Theoretical massNumber of molelcules
Total (without water)94,4916
Polymers94,4916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Protein HEADING DATE 3A
H: Protein HEADING DATE 3A
I: 14-3-3-like protein GF14-C
J: 14-3-3-like protein GF14-C
K: Rice FD homolog OsFD1
L: Rice FD homolog OsFD1


Theoretical massNumber of molelcules
Total (without water)94,4916
Polymers94,4916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.735, 96.647, 99.510
Angle α, β, γ (deg.)68.23, 87.90, 77.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein HEADING DATE 3A / Rice Florigen Hd3a / FT-like protein A


Mass: 18982.418 Da / Num. of mol.: 4 / Fragment: UNP residues 6-170 / Mutation: C43L,C109S,C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HD3A, LOC_Os06g06320, Os06g0157700, OsJ_20191, P0046E09.30, P0702F05.10
Plasmid: pCOLD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q93WI9
#2: Protein
14-3-3-like protein GF14-C / G-box factor 14-3-3 homolog C


Mass: 27151.787 Da / Num. of mol.: 4 / Fragment: UNP residues 1-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: GF14C, LOC_Os08g33370, OJ1124_B05.7, Os08g0430500 / Plasmid: pGEX6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6ZKC0
#3: Protein/peptide
Rice FD homolog OsFD1


Mass: 1111.207 Da / Num. of mol.: 4 / Fragment: C-TERMINAL MOTIF / Source method: obtained synthetically / Details: OsFD1(187-195) fragment, phosphorylated at S192
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 101603 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rsym value: 0.067 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.252 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Code 1WKP for Hd3a, 2O98 for GF14c

1wkp

2o98


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.878 / SU B: 12.325 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27626 7138 7.2 %RANDOM
Rwork0.22728 ---
obs0.23079 92311 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å21.04 Å21.33 Å2
2---1.29 Å20.71 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12974 0 0 777 13751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8711.97217909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8351618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00124.013628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.54715.0262325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.86715100
X-RAY DIFFRACTIONr_chiral_restr0.0780.21998
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02110008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2021.58133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.117213127
X-RAY DIFFRACTIONr_scbond_it3.57435089
X-RAY DIFFRACTIONr_scangle_it5.3884.54782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 522 -
Rwork0.29 6692 -
obs--96.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9919-0.4615-0.130.89240.25120.61790.00050.0076-0.074-0.0336-0.04790.0782-0.0457-0.00260.04730.02550.01530.01360.0155-0.00230.057-22.07134.686-15.289
20.7437-0.07660.00111.1519-0.22990.85370.03280.03910.0750.0030.0430.1158-0.014-0.0418-0.07570.01830.02320.02210.0310.03260.0422-12.66-10.27621.764
30.2037-0.08370.33730.2869-0.22860.95230.01530.07320.03160.0007-0.06620.00370.01540.13080.05080.04120.01930.02320.03890.02010.023217.62324.089-20.359
40.12480.0389-0.1530.7285-0.35620.99760.0388-0.0505-0.04890.0549-0.1345-0.02540.00360.10960.09580.0294-0.02-0.00710.04140.02350.024624.7424.94611.048
50.55490.1021-0.41070.4892-0.01981.39890.0048-0.0539-0.04180.0213-0.00890.0126-0.07710.07570.0040.03410.0040.0040.02430.00660.00737.99-27.16432.962
61.13310.154-0.07831.1118-0.30840.68150.043-0.04140.02030.1696-0.02080.00810.01370.0401-0.02230.05750.01470.01220.01280.00550.0091-11.69223.2129.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 170
2X-RAY DIFFRACTION2B5 - 170
3X-RAY DIFFRACTION3C1 - 235
4X-RAY DIFFRACTION4D1 - 235
5X-RAY DIFFRACTION5G5 - 169
6X-RAY DIFFRACTION6H5 - 170

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