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- PDB-5lu2: Human 14-3-3 sigma complexed with long HSPB6 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 5lu2
TitleHuman 14-3-3 sigma complexed with long HSPB6 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Heat shock protein beta-6Heat shock response
KeywordsSIGNALING PROTEIN / protein-peptide complex / intrinsically disordered protein region(s)
Function / homology
Function and homology information


structural constituent of eye lens / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...structural constituent of eye lens / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / chaperone-mediated protein folding / protein folding chaperone / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / positive regulation of cell growth / regulation of cell cycle / nuclear speck / cadherin binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / mitochondrion / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma ...Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein beta-6 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSluchanko, N.N. / Beelen, S. / Kulikova, A.A. / Weeks, S.D. / Antson, A.A. / Gusev, N.B. / Strelkov, S.V.
CitationJournal: Structure / Year: 2017
Title: Structural Basis for the Interaction of a Human Small Heat Shock Protein with the 14-3-3 Universal Signaling Regulator.
Authors: Sluchanko, N.N. / Beelen, S. / Kulikova, A.A. / Weeks, S.D. / Antson, A.A. / Gusev, N.B. / Strelkov, S.V.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: Heat shock protein beta-6
D: Heat shock protein beta-6


Theoretical massNumber of molelcules
Total (without water)55,3744
Polymers55,3744
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-27 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.060, 78.980, 75.360
Angle α, β, γ (deg.)90.000, 102.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26139.461 Da / Num. of mol.: 2 / Fragment: UNP residues 1-231
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 Heat shock protein beta-6 / Heat shock response / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 1547.760 Da / Num. of mol.: 2 / Fragment: UNP residues 11-23 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14558
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 0.2 M MgCl2 and 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→44 Å / Num. obs: 17880 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 80.39 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.11
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.561.8170.880.261100
2.56-2.641.5371.050.363199.8
2.64-2.711.2621.340.445199.9
2.71-2.80.971.720.659199.8
2.8-2.890.8152.080.735199.6
2.89-2.990.7312.530.761199.7
2.99-3.10.6053.170.789199.8
3.1-3.230.4924.30.832199.3
3.23-3.370.3566.050.89199.9
3.37-3.540.2387.720.954199.7
3.54-3.730.1749.480.974199.6
3.73-3.950.12511.850.986199.7
3.95-4.230.09314.060.989199.3
4.23-4.560.07915.560.991198.8
4.56-50.07815.710.992198.6
5-5.590.08314.060.99198.9
5.59-6.460.07315.620.99199.5
6.46-7.910.05419.160.995199.4
7.91-11.180.03622.090.9971100
11.180.04422.410.996195.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQJ

3iqj


Resolution: 2.5→43.97 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.67 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.653 / SU Rfree Blow DPI: 0.285 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1040 5.82 %RANDOM
Rwork0.209 ---
obs0.211 17876 99.6 %-
Displacement parametersBiso max: 168.74 Å2 / Biso mean: 74.57 Å2 / Biso min: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.1679 Å20 Å20.0114 Å2
2--3.1726 Å20 Å2
3----8.3405 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.5→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 0 127 3880
Biso mean---67.16 -
Num. residues----473
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1396SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes538HARMONIC5
X-RAY DIFFRACTIONt_it3806HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion490SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4422SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3806HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5124HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion20.03
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.291 158 5.51 %
Rwork0.247 2712 -
all-2870 -
obs--99.9 %
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)
12.25930.50060.24522.2302-0.25431.55910.18990.0626-0.3062-0.15560.0026-0.00660.331-0.0101-0.1925-0.2022-0.0048-0.0504-0.10240.0277-0.062830.2243-18.289720.1833
21.3007-0.19820.11382.8095-0.83711.23730.00750.05970.08020.0405-0.0069-0.0277-0.1758-0.0142-0.0006-0.18780.02730.07950.0267-0.0225-0.146831.325919.38120.4848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* D|* }A2 - 231
2X-RAY DIFFRACTION1{ A|* D|* }D13 - 20
3X-RAY DIFFRACTION2{ B|* C|* }B2 - 231
4X-RAY DIFFRACTION2{ B|* C|* }C13 - 20

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