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- PDB-5lum: Alpha-crystallin domain of human HSPB6 patched with its N-termina... -

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Basic information

Entry
Database: PDB / ID: 5lum
TitleAlpha-crystallin domain of human HSPB6 patched with its N-terminal peptide
Components(Heat shock protein beta-6) x 2
KeywordsProtein/Peptide / protein-peptide complex / IDRs / chaperone protein
Function / homology
Function and homology information


structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process ...structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock protein beta-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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, Belgium, United Kingdom, 7items
OrganizationGrant numberCountry
RFBR14-04-00146, 16-04-00016 Russian Federation
FWOG069708N, G093615N and WO03315N Belgium
KULeuven grantOT13/097 Belgium
Wellcome Trust098230 United Kingdom
Biostruct-X283570 Belgium
European UnionFP7/2007-2013 Belgium
European Molecular Biology OrganizationASTF#637-2014 Belgium
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 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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
F: Heat shock protein beta-6
A: Heat shock protein beta-6
G: Heat shock protein beta-6
B: Heat shock protein beta-6
H: Heat shock protein beta-6
C: Heat shock protein beta-6
I: Heat shock protein beta-6
D: Heat shock protein beta-6
J: Heat shock protein beta-6
E: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,19814
Polymers47,81410
Non-polymers3844
Water25214
1
F: Heat shock protein beta-6
A: Heat shock protein beta-6
hetero molecules

F: Heat shock protein beta-6
A: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5108
Polymers19,1254
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4040 Å2
ΔGint-62 kcal/mol
Surface area9920 Å2
MethodPISA
2
G: Heat shock protein beta-6
B: Heat shock protein beta-6
H: Heat shock protein beta-6
C: Heat shock protein beta-6


Theoretical massNumber of molelcules
Total (without water)19,1254
Polymers19,1254
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-9 kcal/mol
Surface area9960 Å2
MethodPISA
3
I: Heat shock protein beta-6
D: Heat shock protein beta-6
J: Heat shock protein beta-6
E: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3186
Polymers19,1254
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-34 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.687, 105.687, 111.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 965.099 Da / Num. of mol.: 5 / Fragment: UNP Residues 2-10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14558
#2: Protein
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 8597.646 Da / Num. of mol.: 5 / Fragment: ACD domain, UNP Residues 72-149
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.77 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Tris-HCl (pH6.5),1.5M ammonium sulfate, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 22684 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 99.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.22
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.6-2.672.6860.890.514199.9
2.67-2.741.9731.270.651100
2.74-2.821.3861.870.8231100
2.82-2.911.0762.440.87199.9
2.91-30.8213.290.918199.9
3-3.110.5394.690.9541100
3.11-3.230.3577.090.9841100
3.23-3.360.2679.980.99199.9
3.36-3.510.18914.080.9951100
3.51-3.680.13218.690.9971100
3.68-3.880.10223.470.9981100
3.88-4.110.08228.180.9981100
4.11-4.40.06136.940.9991100
4.4-4.750.04943.750.9991100
4.75-5.20.04743.760.999199.9
5.2-5.810.0538.850.9991100
5.81-6.710.04542.860.9991100
6.71-8.220.03652.911100
8.22-11.630.02964.7811100
11.630.02963.510.999198.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JUT

4jut


Resolution: 2.6→28.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.318 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1093 4.82 %RANDOM
Rwork0.207 ---
obs0.208 22661 100 %-
Displacement parametersBiso max: 219.72 Å2 / Biso mean: 100.11 Å2 / Biso min: 54.44 Å2
Baniso -1Baniso -2Baniso -3
1--7.571 Å20 Å20 Å2
2---7.571 Å20 Å2
3---15.142 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.6→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 20 14 3409
Biso mean--161.83 79.58 -
Num. residues----435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1129SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes518HARMONIC5
X-RAY DIFFRACTIONt_it3500HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion426SEMIHARMONIC5
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_contact3450SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3500HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4778HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion19.24
LS refinement shellResolution: 2.6→2.73 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.28 134 4.53 %
Rwork0.256 2821 -
all-2955 -
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)
11.36910.19520.61626.21570.0050.9857-0.04060.0359-0.2459-0.2458-0.0180.15350.1473-0.05350.0586-0.26510.01530.0683-0.41850.0106-0.486-64.498-10.710630.4044
25.9671-1.6738-3.24112.5954-0.06134.5946-0.04720.6127-0.4437-0.01780.02290.3349-0.2127-0.63420.0243-0.2560.060.0489-0.396-0.0417-0.3406-52.5288-17.813414.2212
35.2022-4.80891.59393.56570.20726.3314-0.4226-0.21350.74210.69650.4867-0.6436-0.16371.098-0.0641-0.22310.0613-0.084-0.2996-0.1258-0.4029-25.4755-24.512820.2014
45.8348-3.61780.53885.6337-0.24251.81520.56230.65470.225-1.5078-0.6240.5169-0.5561-0.78790.06170.08570.3321-0.1382-0.4134-0.0504-0.7455-61.83541.04040.1958
57.1913-4.9391-0.6016.67011.63437.30290.77330.49640.6884-0.9135-0.318-0.9708-1.529-0.065-0.4553-0.0998-0.02850.2848-0.5750.0982-0.5922-37.6429-4.8955-5.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* F|* }A72 - 149
2X-RAY DIFFRACTION1{ A|* F|* }F2 - 10
3X-RAY DIFFRACTION2{ B|* G|* }B72 - 149
4X-RAY DIFFRACTION2{ B|* G|* }G2 - 10
5X-RAY DIFFRACTION3{ C|* H|* }C72 - 149
6X-RAY DIFFRACTION3{ C|* H|* }H2 - 10
7X-RAY DIFFRACTION4{ D|* I|* }D72 - 149
8X-RAY DIFFRACTION4{ D|* I|* }I2 - 10
9X-RAY DIFFRACTION5{ E|* J|* }E72 - 149
10X-RAY DIFFRACTION5{ E|* J|* }J2 - 10

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