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- PDB-7q16: Human 14-3-3 zeta fused to the BAD peptide including phosphoserine-74 -

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Basic information

Entry
Database: PDB / ID: 7q16
TitleHuman 14-3-3 zeta fused to the BAD peptide including phosphoserine-74
Components14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death
KeywordsSIGNALING PROTEIN / apoptotic regulation / phosphorylation / phosphopeptide binding
Function / homology
Function and homology information


ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / positive regulation of glucokinase activity / BAD-BCL-2 complex / pore complex assembly / Golgi reassembly / synaptic target recognition / glucose catabolic process / respiratory system process ...ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / positive regulation of glucokinase activity / BAD-BCL-2 complex / pore complex assembly / Golgi reassembly / synaptic target recognition / glucose catabolic process / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / type B pancreatic cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / tube formation / Rap1 signalling / activation of cysteine-type endopeptidase activity / cellular response to lipid / negative regulation of protein localization to nucleus / regulation of mitochondrial membrane permeability / positive regulation of mitochondrial membrane potential / AKT phosphorylates targets in the cytosol / positive regulation of T cell differentiation / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of B cell differentiation / GP1b-IX-V activation signalling / NRAGE signals death through JNK / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of proteolysis / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / positive regulation of autophagy / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / ATP metabolic process / RHO GTPases activate PKNs / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of TORC1 signaling / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / intrinsic apoptotic signaling pathway / regulation of ERK1 and ERK2 cascade / release of cytochrome c from mitochondria / positive regulation of epithelial cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / positive regulation of insulin secretion / phospholipid binding / cytokine-mediated signaling pathway / cellular response to nicotine / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / melanosome / glucose homeostasis / cellular response to hypoxia / protein phosphatase binding / angiogenesis / DNA-binding transcription factor binding / vesicle / mitochondrial outer membrane / transmembrane transporter binding / blood microparticle / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation / focal adhesion / glutamatergic synapse / lipid binding / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding
Similarity search - Function
Bcl2-associated agonist of cell death / Pro-apoptotic Bcl-2 protein, BAD / 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
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Bcl2-associated agonist of cell death
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Gushchin, I. / Remeeva, A. / Kovalev, K. / Cooley, R.B.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10031 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of human 14-3-3 zeta complexed with the noncanonical phosphopeptide from proapoptotic BAD.
Authors: Sluchanko, N.N. / Tugaeva, K.V. / Gushchin, I. / Remeeva, A. / Kovalev, K. / Cooley, R.B.
History
DepositionOct 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine
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 / _pdbx_struct_assembly_prop.value / _refine.pdbx_diffrn_id
Revision 1.2Jan 31, 2024Group: 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: 14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death


Theoretical massNumber of molelcules
Total (without water)27,5531
Polymers27,5531
Non-polymers00
Water1,02757
1
A: 14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death

A: 14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death


Theoretical massNumber of molelcules
Total (without water)55,1062
Polymers55,1062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1800 Å2
ΔGint-13 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.698, 112.147, 75.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death / Protein kinase C inhibitor protein 1 / KCIP-1 / BAD / Bcl-2-binding component 6 / Bcl-2-like ...Protein kinase C inhibitor protein 1 / KCIP-1 / BAD / Bcl-2-binding component 6 / Bcl-2-like protein 8 / Bcl2-L-8 / Bcl-xL/Bcl-2-associated death promoter / Bcl2 antagonist of cell death


Mass: 27552.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ, BAD, BBC6, BCL2L8 / Production host: Escherichia coli (E. coli) / References: UniProt: P63104, UniProt: Q92934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4 % w/v PEG 8000, 20 % v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.356→45.062 Å / Num. obs: 11472 / % possible obs: 93.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 52.49 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.7
Reflection shellResolution: 2.356→2.523 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 574 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZFD

6zfd


Resolution: 2.356→45.062 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 583 5.13 %
Rwork0.1968 10771 -
obs0.1989 11354 73.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.3 Å2 / Biso mean: 60.2522 Å2 / Biso min: 29.99 Å2
Refinement stepCycle: final / Resolution: 2.356→45.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 57 1940
Biso mean---55.79 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031911
X-RAY DIFFRACTIONf_angle_d0.5642578
X-RAY DIFFRACTIONf_chiral_restr0.035283
X-RAY DIFFRACTIONf_plane_restr0.002337
X-RAY DIFFRACTIONf_dihedral_angle_d14.5091173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3564-2.59360.3022470.29885824
2.5936-2.96880.30431350.2683249569
2.9688-3.74010.27392050.21863635100
3.7401-45.0620.20761960.16953783100
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)
10.4282-0.4118-0.45270.41290.56111.03940.16970.78260.3955-0.75940.0191-0.1457-0.6032-0.0248-0.00030.5188-0.02660.03460.4420.03760.562728.178318.847-2.5905
20.8586-0.2856-0.50880.7558-0.82091.7959-0.09350.32340.3974-0.15610.1852-0.01260.01950.7238-0.00050.349-0.05720.00810.4638-0.04930.555230.682815.3613.9939
30.27340.1935-0.22430.49480.20140.9909-0.22480.03930.08020.41790.35360.42870.0309-0.0829-0.00040.32730.0154-0.01670.3790.01470.428523.30632.965510.7517
40.1085-0.6468-0.18241.31390.2152-0.0192-0.1081-0.3034-0.21820.61340.1408-1.10010.21670.259-0.00390.47630.0239-0.09570.48670.04540.566431.0317-6.10214.4048
50.611-0.3787-0.44841.0304-1.35533.52350.2596-0.56060.7510.17250.0339-0.5442-1.43040.67530.25770.5634-0.20140.00140.6914-0.22510.902331.81923.936317.4483
60.57010.2855-0.11251.17961.27851.58480.03-0.14810.03540.66460.01410.05860.09950.10160.00020.5206-0.0036-0.0460.5001-0.0510.357225.855210.917520.146
71.9861.5015-0.20221.37190.26270.9725-0.4668-1.16760.34482.03640.6001-0.9299-0.15680.6038-0.00980.86230.0704-0.12710.7806-0.10380.402525.804411.800228.5002
81.56490.24981.10260.35590.30640.5501-0.3013-0.52070.10190.49520.211-0.05670.2167-0.1898-0.00040.70980.0310.16650.5075-0.04830.436215.655212.116424.6893
90.1768-0.171-0.26990.06970.15870.2936-0.1328-0.78380.03640.44910.04030.53160.2157-0.4009-0.00030.76420.02640.27210.7704-0.07850.61957.444413.299328.9513
100.4433-0.10150.31990.1868-0.0651.0416-1.0889-0.17531.7714-0.2872-0.4610.5599-1.99710.4006-0.08631.13770.0537-0.02090.7741-0.09151.05255.874727.109717.3622
110.87880.06180.64840.66260.55070.6965-0.0565-0.051-0.146-0.12250.30420.95230.02540.0561-0.00050.5115-0.05640.18820.6348-0.06140.63385.985410.990819.2467
120.90360.5745-0.88710.3584-0.57380.8884-1.6107-1.03810.10020.23270.3991-0.2282-0.39860.3809-0.18130.47040.0979-0.05410.6660.09590.5185-10.95365.878923.4146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 37 )A16 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 68 )A38 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 103 )A69 - 103
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 111 )A104 - 111
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 135 )A112 - 135
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 159 )A136 - 159
8X-RAY DIFFRACTION8chain 'A' and (resid 160 through 184 )A160 - 184
9X-RAY DIFFRACTION9chain 'A' and (resid 185 through 201 )A185 - 201
10X-RAY DIFFRACTION10chain 'A' and (resid 202 through 210 )A202 - 210
11X-RAY DIFFRACTION11chain 'A' and (resid 211 through 229 )A211 - 229
12X-RAY DIFFRACTION12chain 'A' and (resid 230 through 241 )A230 - 241

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