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- PDB-1qjb: 14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 1) -

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Basic information

Entry
Database: PDB / ID: 1qjb
Title14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 1)
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • PHOSPHOPEPTIDE
KeywordsKINASE INHIBITOR/PEPTIDE / KINASE INHIBITOR-PEPTIDE COMPLEX / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


intracellular protein localization => GO:0008104 / KSRP (KHSRP) binds and destabilizes mRNA / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / Rap1 signalling / TP53 Regulates Metabolic Genes / Golgi reassembly / Interleukin-3, Interleukin-5 and GM-CSF signaling ...intracellular protein localization => GO:0008104 / KSRP (KHSRP) binds and destabilizes mRNA / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / Rap1 signalling / TP53 Regulates Metabolic Genes / Golgi reassembly / Interleukin-3, Interleukin-5 and GM-CSF signaling / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of localization of FOXO transcription factors / host cell membrane / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / regulation of ERK1 and ERK2 cascade / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / lung development / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / Negative regulation of NOTCH4 signaling / regulation of protein stability / intracellular protein localization / melanosome / angiogenesis / protein phosphatase binding / blood microparticle / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / cadherin binding / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / protein kinase binding / negative regulation of apoptotic process / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / 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
Middle T antigen / 14-3-3 protein zeta/delta / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRittinger, K. / Budman, J. / Xu, J. / Volinia, S. / Cantley, L.C. / Smerdon, S.J. / Gamblin, S.J. / Yaffe, M.B.
CitationJournal: Mol.Cell / Year: 1999
Title: Structural Analysis of 14-3-3 Phosphopeptide Complexes Identifies a Dual Role for the Nuclear Export Signal of 14-3-3 in Ligand Binding
Authors: Rittinger, K. / Budman, J. / Xu, J. / Volinia, S. / Cantley, L.C. / Smerdon, S.J. / Gamblin, S.J. / Yaffe, M.B.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
SupersessionSep 15, 1999ID: 14PS
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Q: PHOSPHOPEPTIDE
S: PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)57,4944
Polymers57,4944
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-26.8 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.350, 71.980, 131.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 PROTEIN ZETA/DELTA


Mass: 27777.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PKK233 / Production host: Escherichia coli DH5[alpha] (bacteria) / Variant (production host): F' Iq / References: UniProt: P29312, UniProt: P63104*PLUS
#2: Protein/peptide PHOSPHOPEPTIDE


Mass: 969.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0DOJ9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAINS S AND Q ARE DERIVED FROM THE SEQUENCE, VMRSHSYPPT, FOUND IN MOUSE POLYOMAVIRUS (STRAIN 3) ...CHAINS S AND Q ARE DERIVED FROM THE SEQUENCE, VMRSHSYPPT, FOUND IN MOUSE POLYOMAVIRUS (STRAIN 3) MIDDLE T ANTIGEN (SWS: TAMI_POVM3, P03076)

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.2
Details: COMPLEX WAS CRYSTALLIZED FROM 100 MM MES, PH 6.2, 20 MM MGCL2, 20% ISOPROPANOL AND 15% PEG 4000. IMPROVED CRYSTALS BY MICRO- AND MACROSEEDING INTO 100 MM MES, PH 6.2, 20 MM MGCL2, 15-17% ...Details: COMPLEX WAS CRYSTALLIZED FROM 100 MM MES, PH 6.2, 20 MM MGCL2, 20% ISOPROPANOL AND 15% PEG 4000. IMPROVED CRYSTALS BY MICRO- AND MACROSEEDING INTO 100 MM MES, PH 6.2, 20 MM MGCL2, 15-17% ISOPROPANOL A 12% PEG 4000.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1reservoir
220 mM1reservoirMgCl2
315-17 %isopropanol1reservoir
412 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 37059 / % possible obs: 83.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 41.6
Reflection shell
*PLUS
% possible obs: 41.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 14-3-3 ZETA

Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES FOR CHAINS A AND B WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -5 %RANDOM
Rwork0.21 ---
obs-37059 83.5 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 0 393 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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