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- PDB-7v9b: Crystal Structure of 14-3-3 epsilon with FOXO3a peptide -

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Basic information

Entry
Database: PDB / ID: 7v9b
TitleCrystal Structure of 14-3-3 epsilon with FOXO3a peptide
Components
  • ARG-ARG-ARG-ALA-VAL-SEP-MET-ASP-ASN-SER-ASN
  • YWHAE/FAM22B fusion protein
KeywordsPROTEIN BINDING / FOXO3a / 14-3-3 / 14-3-3 epsilon
Function / homology
Function and homology information


phosphoserine residue binding / regulation of mitotic cell cycle / signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Nuclear Testis protein, N-terminal / NUT protein / 14-3-3 domain / 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 ...Nuclear Testis protein, N-terminal / NUT protein / 14-3-3 domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-323 / IMIDAZOLE / 14-3-3 protein epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMathivanan, S. / Kamariah, N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Acs Omega / Year: 2022
Title: Structure of a 14-3-3 epsilon :FOXO3a pS253 Phosphopeptide Complex Reveals 14-3-3 Isoform-Specific Binding of Forkhead Box Class O Transcription Factor (FOXO) Phosphoproteins.
Authors: Mathivanan, S. / Chunchagatta Lakshman, P.K. / Singh, M. / Giridharan, S. / Sathish, K. / Hurakadli, M.A. / Bharatham, K. / Kamariah, N.
History
DepositionAug 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Nov 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

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Assembly

Deposited unit
A: YWHAE/FAM22B fusion protein
B: ARG-ARG-ARG-ALA-VAL-SEP-MET-ASP-ASN-SER-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4567
Polymers29,6702
Non-polymers7865
Water2,900161
1
A: YWHAE/FAM22B fusion protein
B: ARG-ARG-ARG-ALA-VAL-SEP-MET-ASP-ASN-SER-ASN
hetero molecules

A: YWHAE/FAM22B fusion protein
B: ARG-ARG-ARG-ALA-VAL-SEP-MET-ASP-ASN-SER-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,91114
Polymers59,3394
Non-polymers1,57210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_955-x+4,y,-z+1/21
Unit cell
Length a, b, c (Å)77.880, 81.040, 83.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein YWHAE/FAM22B fusion protein


Mass: 28281.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE/FAM22B fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9K389
#2: Protein/peptide ARG-ARG-ARG-ALA-VAL-SEP-MET-ASP-ASN-SER-ASN


Mass: 1388.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TAMRA Labeled peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 166 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-323 / 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate / 5-Carboxy-N,N'-tetramethyl rhodamine


Mass: 414.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Imidazole pH 8.0, 10 % PEG 4000, 30 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.85→36.46 Å / Num. obs: 22570 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.052 / Rrim(I) all: 0.131 / Rsym value: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3185 / CC1/2: 0.773 / Rpim(I) all: 0.33 / Rrim(I) all: 0.815 / Rsym value: 0.743 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 1.85→36.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.787 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18879 1149 5.1 %RANDOM
Rwork0.16653 ---
obs0.16763 21400 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.092 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---0.57 Å20 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 1.85→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 25 161 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132016
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171907
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6452716
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5994407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3035239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08722.035113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5491517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02424
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_it2.1382.2956
X-RAY DIFFRACTIONr_mcbond_other2.1292.198955
X-RAY DIFFRACTIONr_mcangle_it2.9823.2811192
X-RAY DIFFRACTIONr_mcangle_other2.9833.2831193
X-RAY DIFFRACTIONr_scbond_it3.6622.7161060
X-RAY DIFFRACTIONr_scbond_other3.6612.721061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5413.8991524
X-RAY DIFFRACTIONr_long_range_B_refined7.01427.5222354
X-RAY DIFFRACTIONr_long_range_B_other7.01327.5452355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 84 -
Rwork0.257 1532 -
obs--97.58 %

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