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- PDB-6ef5: 14-3-3 with peptide -

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Basic information

Entry
Database: PDB / ID: 6ef5
Title14-3-3 with peptide
Components
  • 14-3-3 protein zeta/delta
  • ARG-SER-LEU-SEP-ALA-PRO-GLY
  • LYS-LEU-SEP-LEU-GLN
KeywordsSIGNALING PROTEIN / 14-3-3 / Kinase / phosphorylation / protein-protein binding / metabolic signalling protein
Function / homology
Function and homology information


Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / CAMKK-AMPK signaling cascade / establishment of Golgi localization / Rap1 signalling / calmodulin-dependent protein kinase activity / regulation of protein kinase activity ...Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / CAMKK-AMPK signaling cascade / establishment of Golgi localization / Rap1 signalling / calmodulin-dependent protein kinase activity / regulation of protein kinase activity / negative regulation of protein localization to nucleus / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / KSRP (KHSRP) binds and destabilizes mRNA / Activation of RAC1 downstream of NMDARs / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of AMPK downstream of NMDARs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / calcium-mediated signaling / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / cellular response to reactive oxygen species / melanosome / MAPK cascade / protein tyrosine kinase activity / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / calcium ion binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsDhagat, U. / Langendorf, C.G. / Parker, M.W.P. / Oakhill, J.S. / Scott, J.W.
CitationJournal: To Be Published
Title: 14-3-3 with peptide
Authors: Dhagat, U. / Langendorf, C.G. / Oakhill, J.S. / Scott, J.W.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
S: ARG-SER-LEU-SEP-ALA-PRO-GLY
R: LYS-LEU-SEP-LEU-GLN
P: LYS-LEU-SEP-LEU-GLN
Q: ARG-SER-LEU-SEP-ALA-PRO-GLY


Theoretical massNumber of molelcules
Total (without water)115,1108
Polymers115,1108
Non-polymers00
Water25214
1
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
P: LYS-LEU-SEP-LEU-GLN
Q: ARG-SER-LEU-SEP-ALA-PRO-GLY


Theoretical massNumber of molelcules
Total (without water)57,5554
Polymers57,5554
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-30 kcal/mol
Surface area22830 Å2
MethodPISA
2
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
S: ARG-SER-LEU-SEP-ALA-PRO-GLY
R: LYS-LEU-SEP-LEU-GLN


Theoretical massNumber of molelcules
Total (without water)57,5554
Polymers57,5554
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-27 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.691, 94.691, 234.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA-1 - 2292 - 232
21THRTHRBB-1 - 2292 - 232
12SERSERAA-1 - 2302 - 233
22SERSERCC-1 - 2302 - 233
13SERSERAA-1 - 2302 - 233
23SERSERDD-1 - 2302 - 233
14THRTHRBB-1 - 2292 - 232
24THRTHRCC-1 - 2292 - 232
15THRTHRBB-1 - 2292 - 232
25THRTHRDD-1 - 2292 - 232
16SERSERCC-1 - 2302 - 233
26SERSERDD-1 - 2302 - 233

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28059.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide ARG-SER-LEU-SEP-ALA-PRO-GLY


Mass: 767.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RR4*PLUS
#3: Protein/peptide LYS-LEU-SEP-LEU-GLN


Mass: 668.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.1 M MgCl2, 0.001 M NiCl2 and 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018
RadiationMonochromator: Silicon111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.552
11-K, -H, -L20.448
ReflectionResolution: 2.44→82 Å / Num. obs: 44169 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.068 / Rrim(I) all: 0.232 / Net I/σ(I): 7.7 / Num. measured all: 513794 / Scaling rejects: 37
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.44-2.5311.81.0365479046360.3970.3151.0832.4
9.13-8211.90.06104788810.9990.0180.06325.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJB

1qjb


Resolution: 2.44→82 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2385 / WRfactor Rwork: 0.1811 / FOM work R set: 0.814 / SU B: 6.716 / SU ML: 0.158 / SU R Cruickshank DPI: 0.0772 / SU Rfree: 0.0536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 2108 4.8 %RANDOM
Rwork0.1922 ---
obs0.1947 41980 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137 Å2 / Biso mean: 49.913 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1--21.3 Å2-0 Å2-0 Å2
2---21.3 Å2-0 Å2
3---42.6 Å2
Refinement stepCycle: final / Resolution: 2.44→82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 0 14 7349
Biso mean---38.05 -
Num. residues----935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197431
X-RAY DIFFRACTIONr_bond_other_d0.0020.026809
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.97410021
X-RAY DIFFRACTIONr_angle_other_deg1.029315802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71725.226354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.122151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9761543
X-RAY DIFFRACTIONr_chiral_restr0.0960.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021432
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142980.09
12B142980.09
21A140460.1
22C140460.1
31A143460.09
32D143460.09
41B141360.09
42C141360.09
51B146580.09
52D146580.09
61C141480.09
62D141480.09
LS refinement shellResolution: 2.44→2.503 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 137 -
Rwork0.305 3132 -
all-3269 -
obs--99.79 %

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