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- PDB-5wbw: Yeast Hsp104 fragment 1-360 -

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Basic information

Entry
Database: PDB / ID: 5wbw
TitleYeast Hsp104 fragment 1-360
ComponentsHeat shock protein 104Heat shock response
KeywordsCHAPERONE / ATPase
Function / homology
Function and homology information


trehalose metabolism in response to heat stress / TRC complex / cellular heat acclimation / protein folding in endoplasmic reticulum / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein unfolding / nuclear periphery / ADP binding ...trehalose metabolism in response to heat stress / TRC complex / cellular heat acclimation / protein folding in endoplasmic reticulum / post-translational protein targeting to endoplasmic reticulum membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein unfolding / nuclear periphery / ADP binding / unfolded protein binding / protein-folding chaperone binding / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heat shock protein 104
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLee, S.
CitationJournal: Biosci. Rep. / Year: 2017
Title: Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase.
Authors: Lee, J. / Sung, N. / Yeo, L. / Chang, C. / Lee, S. / Tsai, F.T.F.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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: Heat shock protein 104
B: Heat shock protein 104
D: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)118,5993
Polymers118,5993
Non-polymers00
Water43224
1
A: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)39,5331
Polymers39,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)39,5331
Polymers39,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)39,5331
Polymers39,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.556, 75.824, 235.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein 104 / Heat shock response / Protein aggregation-remodeling factor HSP104


Mass: 39533.148 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSP104, YLL026W, L0948 / Production host: Escherichia coli (E. coli) / References: UniProt: P31539
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 25% PEG4000, 50 mM Tris-HCl, 20 mM ammonium citrate
PH range: 8.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0396 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 2.59→49.04 Å / Num. obs: 36873 / % possible obs: 97.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 64.54 Å2 / Rsym value: 0.058 / Net I/σ(I): 16.5
Reflection shellResolution: 2.59→2.68 Å / Num. unique obs: 2973 / Rsym value: 0.346 / % possible all: 80.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 2.6→46.043 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5
RfactorNum. reflection% reflection
Rfree0.2859 2587 7.03 %
Rwork0.2374 --
obs0.2408 36797 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 272.19 Å2 / Biso mean: 97.7463 Å2 / Biso min: 26.33 Å2
Refinement stepCycle: final / Resolution: 2.6→46.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 0 24 7886
Biso mean---71.89 -
Num. residues----1034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027980
X-RAY DIFFRACTIONf_angle_d0.55810816
X-RAY DIFFRACTIONf_chiral_restr0.0211275
X-RAY DIFFRACTIONf_plane_restr0.0041422
X-RAY DIFFRACTIONf_dihedral_angle_d10.6662966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5999-2.64990.44371030.33911415151873
2.6499-2.7040.32681460.31161875202199
2.704-2.76280.35381630.296518822045100
2.7628-2.8270.39731500.305618992049100
2.827-2.89770.34031320.304419472079100
2.8977-2.9760.35291510.274418922043100
2.976-3.06360.34051470.285219212068100
3.0636-3.16250.32231380.288319332071100
3.1625-3.27550.3411330.296919132046100
3.2755-3.40660.3331280.28521919204799
3.4066-3.56150.33311390.27911942208199
3.5615-3.74920.31391610.254819172078100
3.7492-3.9840.28381530.231119262079100
3.984-4.29140.25021510.218419232074100
4.2914-4.72290.23261520.19751956210899
4.7229-5.40540.28451340.22051972210699
5.4054-6.80670.32511410.24231972211398
6.8067-46.04980.21641650.17642006217195
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)
12.85550.66090.47813.93150.47693.5002-0.07450.2789-0.0709-0.19430.09630.23460.20590.0025-00.3814-0.01640.03430.4627-0.05940.4076-16.517614.9065-40.0154
21.89580.05160.13280.656-0.56790.52050.0021-0.2136-0.0814-0.12970.03140.0472-0.0323-0.2382-0.00020.2372-0.00110.02410.3954-0.06180.3292-17.405514.6755-7.2186
30.4337-0.32520.21582.19020.66322.7162-0.0252-0.1001-0.089-0.2363-0.02630.01040.32930.064100.2696-0.00390.04050.3984-0.03930.3968-12.708610.9611-7.5161
40.1101-0.08410.30730.82760.40220.76540.0212-0.6518-0.04970.3472-0.0388-0.41920.41920.29940.00010.49160.0979-0.04510.72810.13790.5078-9.8237.1578.5301
51.2514-1.37920.45511.1779-0.73430.4054-0.0111-0.1352-0.1624-0.0510.1997-0.01550.02140.3067-00.83190.14680.08260.4674-0.03920.6788-5.1098-26.5565-11.4297
60.1282-0.7113-0.52742.451-0.99672.7362-0.0113-0.1132-0.32960.31620.26410.3694-0.5349-0.63860.02470.84910.13310.16270.45720.05730.7007-14.1747-19.5364-18.5459
71.0837-0.1461-0.63690.76920.46270.8765-0.19873.57771.7012-0.51020.3489-1.2219-0.2377-0.2942-0.01191.2527-0.17730.05911.29630.73941.699-5.0663-22.3058-54.4559
82.22870.5326-1.16951.8859-1.61291.1869-0.28960.320.35-0.13060.2010.11460.0733-0.2055-0.01790.5852-0.0586-0.11550.37480.10540.4492-13.9377-32.2527-49.3183
92.8325-0.71330.46794.6866-0.49912.59380.0526-0.10960.3887-0.190.1145-0.5-0.3250.35180.00050.5642-0.11620.02430.4993-0.07680.6361-50.759732.7658-42.3902
101.9129-0.32952.06172.5231-0.34623.18590.43160.1864-0.2276-0.19880.2623-0.07330.7295-0.19330.14690.5644-0.0738-0.1580.4473-0.08290.2797-43.1042.4923-23.0533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 148 )A6 - 148
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 217 )A149 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 317 )A218 - 317
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 343 )A318 - 343
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 89 )B6 - 89
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 179 )B90 - 179
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 241 )B180 - 241
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 356 )B242 - 356
9X-RAY DIFFRACTION9chain 'D' and (resid 4 through 170 )D4 - 170
10X-RAY DIFFRACTION10chain 'D' and (resid 171 through 356 )D171 - 356

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