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- PDB-5lu1: Human 14-3-3 sigma CLU3 mutant complexed with short HSPB6 phospho... -

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Basic information

Entry
Database: PDB / ID: 5lu1
TitleHuman 14-3-3 sigma CLU3 mutant complexed with short HSPB6 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Heat shock protein beta-6
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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / chaperone-mediated protein folding / RHO GTPases activate PKNs / protein folding chaperone / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / 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 / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / unfolded protein binding / protein-folding chaperone binding / protein refolding / response to heat / 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: 2.4 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
E: 14-3-3 protein sigma
F: 14-3-3 protein sigma
G: Heat shock protein beta-6
H: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,31512
Polymers108,8268
Non-polymers4894
Water6,503361
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: Heat shock protein beta-6
D: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6576
Polymers54,4134
Non-polymers2442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-21 kcal/mol
Surface area22080 Å2
MethodPISA
2
E: 14-3-3 protein sigma
F: 14-3-3 protein sigma
G: Heat shock protein beta-6
H: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6576
Polymers54,4134
Non-polymers2442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-22 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.610, 104.010, 123.070
Angle α, β, γ (deg.)90.000, 93.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26257.600 Da / Num. of mol.: 4 / Fragment: UNP residues 1-231 / Mutation: CLU3
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 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 949.003 Da / Num. of mol.: 4 / Fragment: UNP residues 13-20 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14558
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris propane (pH 6.5), 0.2 M NaNO3 and 20% PEG 3350

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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: 2.4→48 Å / Num. obs: 54513 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 66.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.61
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.4-2.461.5330.90.311199.9
2.46-2.531.2891.120.4061100
2.53-2.61.0541.40.561199.8
2.6-2.680.8481.80.654199.8
2.68-2.770.6362.330.745199.9
2.77-2.870.4993.020.834199.8
2.87-2.980.383.880.899199.9
2.98-3.10.2725.250.942199.8
3.1-3.240.1987.140.962199.8
3.24-3.390.1519.070.978199.5
3.39-3.580.10911.770.986199.1
3.58-3.790.08714.150.991199.4
3.79-4.060.06816.860.993198.8
4.06-4.380.06118.620.994199.1
4.38-4.80.05320.230.995199.1
4.8-5.370.05320.040.995199.5
5.37-6.20.05319.790.995199.3
6.2-7.590.04422.810.996199.7
7.59-10.730.03525.630.998199.7
10.730.03225.940.997196.6

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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: 2.4→47.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2718 4.99 %RANDOM
Rwork0.184 ---
obs0.186 54511 99.6 %-
Displacement parametersBiso max: 201.42 Å2 / Biso mean: 72.11 Å2 / Biso min: 33.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.0067 Å20 Å26.6428 Å2
2--6.0125 Å20 Å2
3----7.0193 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.4→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 32 361 7842
Biso mean--124.99 70.53 -
Num. residues----941
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2761SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes219HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1072HARMONIC5
X-RAY DIFFRACTIONt_it7587HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion975SEMIHARMONIC5
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_contact9093SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7587HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10217HARMONIC21.64
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion18.81
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 201 5.01 %
Rwork0.229 3808 -
all-4009 -
obs--99.97 %
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)
11.05390.60270.53.28391.00661.38750.16620.1033-0.24610.20240.0625-0.16780.32320.0411-0.22870.03050.0517-0.0701-0.04670.0285-0.006918.012-18.62114.7127
21.9633-0.69150.46392.6202-0.27181.3173-0.1696-0.0630.20650.17920.00730.0939-0.1197-0.00210.1623-0.1151-0.0293-0.0003-0.052-0.0414-0.040511.75219.11718.767
32.331-0.34690.53352.77781.11232.62210.0528-0.42940.37820.06770.1391-0.2671-0.39240.2297-0.1920.031-0.09720.05950.1292-0.1011-0.015241.888-27.3749.029
41.95180.84620.32052.40240.21321.7841-0.0554-0.2493-0.30080.00060.10980.03240.1495-0.0319-0.0544-0.08940.02670.0080.02040.0277-0.024633.358-63.23838.999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* C|* }A2 - 231
2X-RAY DIFFRACTION1{ A|* C|* }C13 - 20
3X-RAY DIFFRACTION2{ B|* D|* }B-2 - 231
4X-RAY DIFFRACTION2{ B|* D|* }D13 - 20
5X-RAY DIFFRACTION3{ E|* G|* }E-1 - 231
6X-RAY DIFFRACTION3{ E|* G|* }G13 - 20
7X-RAY DIFFRACTION4{ F|* H|* }F-2 - 231
8X-RAY DIFFRACTION4{ F|* H|* }H13 - 20

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