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- PDB-4hkc: 14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4... -

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Basic information

Entry
Database: PDB / ID: 4hkc
Title14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4 peptide
Components
  • 14-3-3 protein zeta/delta
  • alpha-4 integrin derived phosphorylated peptide
KeywordsSIGNALING PROTEIN/PEPTIDE / 14-3-3 / all-helical protein / regulatory / alpha-4 integrin tail / phosphorylation / SIGNAL TRANSDUCTION / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Golgi reassembly ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Golgi reassembly / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / protein antigen binding / establishment of Golgi localization / leukocyte tethering or rolling / RUNX3 Regulates Immune Response and Cell Migration / Rap1 signalling / positive regulation of endothelial cell apoptotic process / heterotypic cell-cell adhesion / negative regulation of protein localization to nucleus / integrin complex / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / neuron projection extension / KSRP (KHSRP) binds and destabilizes mRNA / leukocyte cell-cell adhesion / negative regulation of vasoconstriction / GP1b-IX-V activation signalling / receptor clustering / endodermal cell differentiation / cellular response to cytokine stimulus / fibronectin binding / 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 / positive regulation of T cell migration / cellular response to glucose starvation / Integrin cell surface interactions / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / coreceptor activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / cell adhesion molecule binding / cell-matrix adhesion / negative regulation of innate immune response / substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of ERK1 and ERK2 cascade / B cell differentiation / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / Cell surface interactions at the vascular wall / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / melanosome / integrin binding / growth cone / blood microparticle / DNA-binding transcription factor binding / vesicle / Potential therapeutics for SARS / transmembrane transporter binding / cadherin binding / external side of plasma membrane / protein phosphorylation / focal adhesion / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor ...: / Integrin alpha Ig-like domain 3 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / 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
Integrin alpha-4 / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBonet, R. / Campbell, I.D.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Characterization of 14-3-3-zeta Interactions with integrin tails
Authors: Bonet, R. / Vakonakis, I. / Campbell, I.D.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Apr 21, 2021Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: alpha-4 integrin derived phosphorylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0793
Polymers31,9872
Non-polymers921
Water2,180121
1
A: 14-3-3 protein zeta/delta
B: alpha-4 integrin derived phosphorylated peptide
hetero molecules

A: 14-3-3 protein zeta/delta
B: alpha-4 integrin derived phosphorylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1576
Polymers63,9734
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4290 Å2
ΔGint-26 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.030, 111.600, 72.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 28188.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag followed by a 3C protease cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63104
#2: Protein/peptide alpha-4 integrin derived phosphorylated peptide / CD49 antigen-like family member D / Integrin alpha-IV / VLA-4 subunit alpha


Mass: 3797.991 Da / Num. of mol.: 1 / Fragment: UNP residues 1003-1032 / Source method: obtained synthetically
Details: Chemically synthesized peptide corresponding to alpha-4 integrin tail
Source: (synth.) Homo sapiens (human) / References: UniProt: P13612
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na HEPES (pH 7.5), 25% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.2→44.5 Å / Num. all: 18798 / Num. obs: 18798 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 49.47 Å2 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2725 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O02

2o02


Resolution: 2.2→34.8 Å / Cor.coef. Fo:Fc: 0.9507 / Cor.coef. Fo:Fc free: 0.9375 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 965 5.15 %RANDOM
Rwork0.197 ---
all0.1991 18798 --
obs0.1991 18727 99.4 %-
Displacement parametersBiso mean: 60.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.4036 Å20 Å20 Å2
2--0.2998 Å20 Å2
3----0.7034 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 6 121 2022
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022589HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d710SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes268HARMONIC5
X-RAY DIFFRACTIONt_it1925HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion17.2
X-RAY DIFFRACTIONt_chiral_improper_torsion249SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2414SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2379 171 5.7 %
Rwork0.2274 2827 -
all0.228 2998 -
obs--99.4 %
Refinement TLS params.Method: refined / Origin x: 22.1337 Å / Origin y: 7.89 Å / Origin z: 17.4031 Å
111213212223313233
T-0.0376 Å20.0065 Å2-0.187 Å2--0.1533 Å20.0198 Å2---0.0456 Å2
L0.8825 °2-0.3647 °2-0.4773 °2-2.6943 °20.6138 °2--1.535 °2
S-0.0858 Å °-0.1571 Å °0.0414 Å °0.7998 Å °0.0807 Å °-0.6837 Å °-0.0055 Å °0.1525 Å °0.0051 Å °
Refinement TLS groupSelection details: { A|2 - A|230 }

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