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- PDB-4i88: R107G HSP16.5 -

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Basic information

Entry
Database: PDB / ID: 4i88
TitleR107G HSP16.5
ComponentsSmall heat shock protein HSP16.5
KeywordsCHAPERONE / alpha-B domain
Function / homology
Function and homology information


protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat / protein stabilization / protein-containing complex ...protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat / protein stabilization / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
: / 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
Small heat shock protein HSP16.5
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPohl, E. / Williamson, I.R. / Quinlan, R.A.
CitationJournal: Philos Trans R Soc Lond B Biol Sci / Year: 2013
Title: Changes in the quaternary structure and function of MjHSP16.5 attributable to deletion of the IXI motif and introduction of the substitution, R107G, in the α-crystallin domain.
Authors: Roy A Quinlan / Yan Zhang / Andrew Lansbury / Ian Williamson / Ehmke Pohl / Fei Sun /
Abstract: The archael small heat-shock protein (sHSP), MjHSP16.5, forms a 24-subunit oligomer with octahedral symmetry. Here, we demonstrate that the IXI motif present in the C-terminal domain is necessary for ...The archael small heat-shock protein (sHSP), MjHSP16.5, forms a 24-subunit oligomer with octahedral symmetry. Here, we demonstrate that the IXI motif present in the C-terminal domain is necessary for the oligomerization of MjHSP16.5. Removal increased the in vitro chaperone activity with citrate synthase as the client protein. Less predictable were the effects of the R107G substitution in MjHSP16.5 because of the differences in the oligomerization of metazoan and non-metazoan sHSPs. We present the crystal structure for MjHSP16.5 R107G and compare this with an improved (2.5 Å) crystal structure for wild-type (WT) MjHSP16.5. Although no significant structural differences were found in the crystal, using cryo-electron microscopy, we identified two 24mer species with octahedral symmetry for the WT MjHSP16.5 both at room temperature and at 60°C, all showing two major species with the same diameter of 12.4 nm. Similarly, at room temperature, there are also two kinds of 12.4 nm oligomers for R107G MjHSP16.5, but in the 60°C sample, a larger 24mer species with a diameter of 13.6 nm was observed with significant changes in the fourfold symmetry axis and dimer-dimer interface. This highly conserved arginine, therefore, contributes to the quaternary organization of non-metazoan sHSP oligomers. Potentially, the R107G substitution has functional consequences as R107G MjHSP16.5 was far superior to the WT protein in protecting βL-crystallin against heat-induced aggregation.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5


Theoretical massNumber of molelcules
Total (without water)131,7608
Polymers131,7608
Non-polymers00
Water72140
1
A: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5

A: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5

A: Small heat shock protein HSP16.5
B: Small heat shock protein HSP16.5
C: Small heat shock protein HSP16.5
D: Small heat shock protein HSP16.5
E: Small heat shock protein HSP16.5
F: Small heat shock protein HSP16.5
G: Small heat shock protein HSP16.5
H: Small heat shock protein HSP16.5


Theoretical massNumber of molelcules
Total (without water)395,28024
Polymers395,28024
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area75850 Å2
ΔGint-317 kcal/mol
Surface area119890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.600, 173.600, 103.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Small heat shock protein HSP16.5


Mass: 16469.990 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57733
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 mM CaCl2, 20 mM sodium acetate, 30-35% MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 27031 / Num. obs: 26318 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.924 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.848 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1314 5 %RANDOM
Rwork0.19469 ---
all0.19768 27031 --
obs0.19768 26318 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6985 0 0 40 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9939568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8995903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.22326.471272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.955151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2171524
X-RAY DIFFRACTIONr_chiral_restr0.1180.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.7461.54524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.23627368
X-RAY DIFFRACTIONr_scbond_it15.00732557
X-RAY DIFFRACTIONr_scangle_it19.5324.52200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.54 92 -
Rwork0.472 1905 -
obs--99.85 %

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