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- PDB-5ltw: Complex of human 14-3-3 sigma CLU1 mutant with phosphorylated hea... -

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Basic information

Entry
Database: PDB / ID: 5ltw
TitleComplex of human 14-3-3 sigma CLU1 mutant with phosphorylated heat shock protein B6
Components
  • 14-3-3 protein sigma
  • Heat shock protein beta-6
KeywordsPROTEIN BINDING / protein-protein complex / intrinsically disordered protein region(s)
Function / homology
Function and homology information


structural constituent of eye lens / negative regulation of cardiac muscle cell apoptotic process / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors ...structural constituent of eye lens / negative regulation of cardiac muscle cell apoptotic process / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / : / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / protein folding chaperone / positive regulation of cell adhesion / protein sequestering activity / 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 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / intracellular protein localization / unfolded protein binding / protein-folding chaperone binding / regulation of protein localization / response to heat / protein refolding / positive regulation of cell growth / regulation of cell cycle / nuclear speck / cadherin binding / protein kinase binding / negative regulation of apoptotic process / 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 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...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 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
Similarity search - Domain/homology
NICKEL (II) ION / Heat shock protein beta-6 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsSluchanko, N.N. / Beelen, S. / Kulikova, A.A. / Weeks, S.D. / Antson, A.A. / Gusev, N.B. / Strelkov, S.V.
Funding support Russian Federation, United Kingdom, Belgium, 4items
OrganizationGrant numberCountry
Russian Foundation for Basic Research14-04-00146 Russian Federation
Wellcome Trust098230 United Kingdom
FWOG069708N, G093615N, WO03315N Belgium
Russian Foundation for Basic Research16-04-00016 Russian Federation
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
I: 14-3-3 protein sigma
J: 14-3-3 protein sigma
K: Heat shock protein beta-6
L: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,92721
Polymers255,01812
Non-polymers9099
Water00
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)85,3097
Polymers85,0064
Non-polymers3033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-33 kcal/mol
Surface area32910 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)85,3097
Polymers85,0064
Non-polymers3033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-37 kcal/mol
Surface area33310 Å2
MethodPISA
3
I: 14-3-3 protein sigma
J: 14-3-3 protein sigma
K: Heat shock protein beta-6
L: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3097
Polymers85,0064
Non-polymers3033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-30 kcal/mol
Surface area33870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.060, 341.290, 144.550
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 sigma / Epithelial cell marker protein 1 / Stratifin / CLU1


Mass: 26257.537 Da / Num. of mol.: 6 / Mutation: K162A, K163A, E164A
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
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 16245.406 Da / Num. of mol.: 6 / Fragment: UNP Residues 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB6 / Production host: Escherichia coli (E. coli) / References: UniProt: O14558
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 0.2 M LiCl, 17% PEG 6000 and 2 mM DTT

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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: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 4.5→45.2 Å / Num. obs: 18727 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 199.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.314 / Net I/σ(I): 5.76
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
4.5-4.622.0871.080.337199.9
4.62-4.742.0021.20.389199.9
4.74-4.881.791.280.393199.9
4.88-5.031.61.480.429199.8
5.03-5.21.5491.50.4841100
5.2-5.381.7721.360.391100
5.38-5.581.4841.630.544199.9
5.58-5.811.2981.880.568199.8
5.81-6.071.0452.460.6491100
6.07-6.360.723.390.817199.9
6.36-6.710.62240.851100
6.71-7.120.4595.260.927199.8
7.12-7.610.3456.850.966199.9
7.61-8.220.18911.330.987199.6
8.22-90.12615.330.994199.5
9-10.060.08819.590.997199.7
10.06-11.620.07721.520.997199
11.62-14.230.07222.870.997199
14.23-20.130.06523.690.998199
20.130.06622.170.998185

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQJ

3iqj


Resolution: 4.5→45.17 Å / Cor.coef. Fo:Fc: 0.731 / Cor.coef. Fo:Fc free: 0.73 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.035
RfactorNum. reflection% reflectionSelection details
Rfree0.256 934 4.99 %RANDOM
Rwork0.236 ---
obs0.237 18722 99.7 %-
Displacement parametersBiso mean: 86.66 Å2
Baniso -1Baniso -2Baniso -3
1--56.8815 Å20 Å20 Å2
2---15.6391 Å20 Å2
3---72.5205 Å2
Refine analyzeLuzzati coordinate error obs: 0.91 Å
Refinement stepCycle: LAST / Resolution: 4.5→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15773 0 111 0 15884
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0921886HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5699SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes436HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2326HARMONIC5
X-RAY DIFFRACTIONt_it16183HARMONIC20
X-RAY DIFFRACTIONt_nbd11SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2048SEMIHARMONIC5
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_contact18336SEMIHARMONIC4
LS refinement shellResolution: 4.5→4.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.276 148 4.95 %
Rwork0.243 2839 -
all0.244 2987 -
obs--99.87 %
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)
15.12241.65550.67012.2638-0.04222.79380.1164-0.5203-0.04640.5442-0.1655-0.1555-0.1952-0.41550.04910.1744-0.0025-0.05460.0184-0.0235-0.257936.949333.760457.2268
22.9987-2.91041.13517.86130.11524.8406-0.0369-0.53070.2235-0.16960.41840.1955-0.5442-0.0184-0.38150.0028-0.1520.0397-0.21310.152-0.236621.236232.183920.5067
32.203-0.11671.24014.13920.05742.8143-0.2937-0.25150.5442-0.07930.04570.2934-0.5015-0.00340.2480.26480.1520.0651-0.05070.1520.30414.035876.6211-1.7347
43.60540.99822.77214.8601-2.20456.4970.21890.54420.5442-0.4944-0.3253-0.207-0.4649-0.32840.10640.3040.152-0.1520.0598-0.00490.30444.983567.36220.9718
52.0953-0.32440.03411.29050.9364.07510.13110.2566-0.1401-0.3802-0.1223-0.2203-0.16770.039-0.0088-0.3040.02170.152-0.3040.152-0.30438.14117.2365-29.6241
68.31540.41571.14870.67770.42381.7896-0.3364-0.01490.54420.46560.12850.0958-0.23310.48320.2079-0.0502-0.0392-0.02560.18210.0203-0.11949.48528.9551-55.2914
70.01172.9104-2.91047.8542-2.910400.0790.136-0.54420.07290.3862-0.16070.01840.022-0.4652-0.2556-0.1317-0.1520.10680.152-0.3049.557918.8637-9.6706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ E|* F|* H|13 - H|24 G|13 - G|24 }
2X-RAY DIFFRACTION2{ G|68 - G|149 H|68 - H|149 G|1 - G|12 D|1 - D|12 G|25 - G|40 }
3X-RAY DIFFRACTION3{ A|* B|* C|13 - C|24 D|13 - D|24 }
4X-RAY DIFFRACTION4{ C|68 - C|149 D|68 - D|149 C|1 - C|12 H|1 - H|12 C|25 - C|40 }
5X-RAY DIFFRACTION5{ I|* J|* L|13 - L|24 K|13 - K|24 }
6X-RAY DIFFRACTION6{ K|68 - K|149 L|68 - L|149 K|1 - K|12 K|25 - K|40 }
7X-RAY DIFFRACTION7{ L|1 - L|12 }

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