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- PDB-5u2u: Crystal structure of the Hsp104 N-terminal domain from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 5u2u
TitleCrystal structure of the Hsp104 N-terminal domain from Saccharomyces cerevisiae
ComponentsHeat shock protein 104Heat shock response
KeywordsPROTEIN BINDING / Saccharomyces cerevisiae / Hsp104 / N-terminal domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsWang, P. / Li, J. / Sha, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM080261 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structures of Hsp104 N-terminal domains from Saccharomyces cerevisiae and Candida albicans suggest the mechanism for the function of Hsp104 in dissolving prions.
Authors: Wang, P. / Li, J. / Weaver, C. / Lucius, A. / Sha, B.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 104
B: Heat shock protein 104
C: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)56,6293
Polymers56,6293
Non-polymers00
Water19811
1
A: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)18,8761
Polymers18,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)18,8761
Polymers18,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock protein 104


Theoretical massNumber of molelcules
Total (without water)18,8761
Polymers18,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.587, 66.255, 74.577
Angle α, β, γ (deg.)90.00, 107.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18876.271 Da / Num. of mol.: 3
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) / Strain (production host): BL21 / References: UniProt: P31539
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 1000, 50 mM Tris-HCl pH 8.5, 20 mM ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 22041 / % possible obs: 96.2 % / Redundancy: 3.5 % / Net I/σ(I): 30.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.541→38.481 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.256 1975 9.04 %
Rwork0.1994 --
obs0.2046 21839 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.541→38.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 0 11 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093873
X-RAY DIFFRACTIONf_angle_d1.3485248
X-RAY DIFFRACTIONf_dihedral_angle_d15.691473
X-RAY DIFFRACTIONf_chiral_restr0.054600
X-RAY DIFFRACTIONf_plane_restr0.008696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5411-2.60460.31321200.22121207X-RAY DIFFRACTION83
2.6046-2.67510.30481400.22551437X-RAY DIFFRACTION95
2.6751-2.75370.28411400.22341432X-RAY DIFFRACTION96
2.7537-2.84260.29561450.22211420X-RAY DIFFRACTION97
2.8426-2.94420.31851390.22651439X-RAY DIFFRACTION97
2.9442-3.0620.2971430.23421435X-RAY DIFFRACTION97
3.062-3.20130.32521450.23341443X-RAY DIFFRACTION97
3.2013-3.370.27081460.22541458X-RAY DIFFRACTION97
3.37-3.5810.27711410.21261426X-RAY DIFFRACTION96
3.581-3.85720.26111440.20761436X-RAY DIFFRACTION96
3.8572-4.2450.22231430.18491432X-RAY DIFFRACTION96
4.245-4.85820.22841440.16931435X-RAY DIFFRACTION96
4.8582-6.11680.22741420.19011435X-RAY DIFFRACTION95
6.1168-38.4850.21181430.16331429X-RAY DIFFRACTION91

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