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- PDB-6amn: Crystal Structure of Hsp104 N Domain -

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Basic information

Entry
Database: PDB / ID: 6amn
TitleCrystal Structure of Hsp104 N Domain
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 / MAD / Resolution: 2.816 Å
AuthorsLee, S.
CitationJournal: Sci Rep / Year: 2017
Title: Overlapping and Specific Functions of the Hsp104 N Domain Define Its Role in Protein Disaggregation.
Authors: Lee, J. / Sung, N. / Mercado, J.M. / Hryc, C.F. / Chang, C. / Lee, S. / Tsai, F.T.F.
History
DepositionAug 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: 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


Theoretical massNumber of molelcules
Total (without water)39,0771
Polymers39,0771
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.096, 179.096, 69.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 39076.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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.: 4 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 33% PEG400, 50mM HEPES-HCl pH 7.2, 150mM Sodium formate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: Brandeis B4 / Detector: CCD / Date: Mar 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→41.53 Å / Num. obs: 14077 / % possible obs: 84.2 % / Redundancy: 14.7 % / Rsym value: 0.076 / Net I/σ(I): 17.6
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 207 / Rsym value: 0.386 / % possible all: 12.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.816→41.526 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 710 5.06 %
Rwork0.2102 13326 -
obs0.2136 14036 85.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.35 Å2 / Biso mean: 94.1028 Å2 / Biso min: 38.68 Å2
Refinement stepCycle: final / Resolution: 2.816→41.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 0 4 2725
Biso mean---74.25 -
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022761
X-RAY DIFFRACTIONf_angle_d0.3993732
X-RAY DIFFRACTIONf_chiral_restr0.038433
X-RAY DIFFRACTIONf_plane_restr0.004490
X-RAY DIFFRACTIONf_dihedral_angle_d12.0091713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8163-3.03370.3978480.30521125117336
3.0337-3.33890.3631490.27372843299293
3.3389-3.82170.29631630.2263049321299
3.8217-4.81380.22751580.1853098325699
4.8138-41.53070.28391920.20343211340398
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)
18.294-0.7662-1.0985.56030.53044.9191-0.2454-0.2295-0.33790.14580.1654-0.51380.20570.11690.03070.50710.24790.01790.466-0.03110.45858.622153.085545.4177
25.3998-5.3476-1.52535.31951.0241.77560.360.9066-0.8558-0.5802-0.65490.2605-0.1786-0.13230.32470.6440.15640.09090.7301-0.04360.714139.124355.040641.137
35.9863-0.99390.87143.6739-0.46145.60770.24561.0131-1.0042-0.7406-0.29020.49050.4621-0.4370.00140.59440.0727-0.04180.7645-0.28550.672422.611966.350133.9541
49.50830.19593.0753.301-1.05365.3716-0.0820.18770.08940.1124-0.27040.38-0.1122-0.38570.30730.48930.06750.09610.7042-0.12120.524619.365176.842136.0957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 148 )A4 - 148
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 170 )A149 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 273 )A171 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 352 )A274 - 352

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