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- PDB-6qdr: Crystal structure of 14-3-3sigma in complex with a PAK6 pT99 phos... -

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Basic information

Entry
Database: PDB / ID: 6qdr
TitleCrystal structure of 14-3-3sigma in complex with a PAK6 pT99 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Serine/threonine-protein kinase PAK 6
KeywordsCHAPERONE / Neuron Regeneration / PPI / phosphorylation
Function / homology
Function and homology information


RHOD GTPase cycle / Activation of RAC1 / RHOV GTPase cycle / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / CDC42 GTPase cycle / Regulation of localization of FOXO transcription factors ...RHOD GTPase cycle / Activation of RAC1 / RHOV GTPase cycle / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / CDC42 GTPase cycle / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / RHOH GTPase cycle / regulation of MAPK cascade / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / protein export from nucleus / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of protein localization / positive regulation of protein export from nucleus / cytoskeleton organization / RAC1 GTPase cycle / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / cellular response to starvation / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / fibrillar center / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / non-specific serine/threonine protein kinase / postsynaptic density / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / protein kinase binding / signal transduction / : / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase PAK 6 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 14-3-3 domain / Delta-Endotoxin; domain 1 ...Serine/threonine-protein kinase PAK 6 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 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 / Protein kinase 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 sigma / Serine/threonine-protein kinase PAK 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.615 Å
AuthorsAndrei, S.A. / Kaplan, A. / Fournier, A.E. / Ottman, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchECHO -STIP 717.014.001 Netherlands
CitationJournal: Cell Chem Biol / Year: 2020
Title: Polypharmacological Perturbation of the 14-3-3 Adaptor Protein Interactome Stimulates Neurite Outgrowth.
Authors: Kaplan, A. / Andrei, S.A. / van Regteren Altena, A. / Simas, T. / Banerjee, S.L. / Kato, N. / Bisson, N. / Higuchi, Y. / Ottmann, C. / Fournier, A.E.
History
DepositionJan 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 19, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]
Revision 2.1Aug 11, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0499
Polymers27,8402
Non-polymers2097
Water7,674426
1
A: 14-3-3 protein sigma
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: 14-3-3 protein sigma
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09818
Polymers55,6814
Non-polymers41814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5150 Å2
ΔGint-115 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.479, 112.397, 62.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

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Components

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

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Serine/threonine-protein kinase PAK 6 / PAK-5 / p21-activated kinase 6 / PAK-6


Mass: 1297.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9NQU5, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 433 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.19 M CaCl2, 5% v/v glycerol, 28 % PEG400, 0.095 M HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.615→41.84 Å / Num. obs: 31456 / % possible obs: 83.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 6.27 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.615-1.641.11.8690.2460.3473.7
4.38-41.855.634.820350.0140.035100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.24 Å41.84 Å
Translation5.24 Å41.84 Å

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Processing

Software
NameVersionClassification
xia2data reduction
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.615→41.839 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.67
RfactorNum. reflection% reflection
Rfree0.1822 1539 4.9 %
Rwork0.1512 --
obs0.1527 31435 83.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.88 Å2 / Biso mean: 16.7577 Å2 / Biso min: 4.6 Å2
Refinement stepCycle: final / Resolution: 1.615→41.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 7 426 2314
Biso mean--20.21 27.79 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6153-1.66740.318670.21692202277
1.6674-1.7270.2427640.21231184124837
1.727-1.79610.22181280.19152353248173
1.7961-1.87790.21011560.17783165332198
1.8779-1.97690.1681420.16232383380100
1.9769-2.10070.18251670.14432493416100
2.1007-2.26290.18881650.138932353400100
2.2629-2.49060.19051880.137832573445100
2.4906-2.8510.17981770.143732603437100
2.851-3.59160.17041770.138732983475100
3.5916-41.8530.16821680.157734373605100

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