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- PDB-3c7n: Structure of the Hsp110:Hsc70 Nucleotide Exchange Complex -

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Basic information

Entry
Database: PDB / ID: 3c7n
TitleStructure of the Hsp110:Hsc70 Nucleotide Exchange Complex
Components
  • Heat shock cognate
  • Heat shock protein homolog SSE1Heat shock response
KeywordsCHAPERONE/CHAPERONE / chaperone / HSP110 / HSP70 / HSC70 / molecular chaperone / ATP state / acetylation / ATP-binding / ADP / calmodulin binding / cytoplasm / mucleotide binding / phosphorylation / stress response / Calmodulin-binding / Nucleotide-binding / Phosphoprotein / Nucleus / TRANSCRIPTION / CHAPERONE-CHAPERONE COMPLEX
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / Neutrophil degranulation / postsynaptic cytosol / proteasomal ubiquitin-independent protein catabolic process / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / peptide binding / ATP-dependent protein folding chaperone / spliceosomal complex / terminal bouton / mRNA processing / autophagy / melanosome / protein-macromolecule adaptor activity / protein folding / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / calmodulin binding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Heat shock cognate 71 kDa protein / Heat shock protein homolog SSE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.115 Å
AuthorsSchuermann, J.P. / Jiang, J. / Hart, P.J. / Sousa, R.
CitationJournal: Mol.Cell / Year: 2008
Title: Structure of the Hsp110:Hsc70 nucleotide exchange machine
Authors: Schuermann, J.P. / Jiang, J. / Cuellar, J. / Llorca, O. / Wang, L. / Gimenez, L.E. / Jin, S. / Taylor, A.B. / Demeler, B. / Morano, K.A. / Hart, P.J. / Valpuesta, J.M. / Lafer, E.M. / Sousa, R.
History
DepositionFeb 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein homolog SSE1
B: Heat shock cognate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,08314
Polymers135,6232
Non-polymers1,46012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-126.3 kcal/mol
Surface area52110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.533, 169.501, 87.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heat shock protein homolog SSE1 / Heat shock response / Chaperone protein MSI3


Mass: 74542.055 Da / Num. of mol.: 1 / Fragment: residues 1-666
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSE1, MSI3 / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32589
#2: Protein Heat shock cognate / Heat shock 70 kDa protein 8


Mass: 61080.906 Da / Num. of mol.: 1 / Fragment: residues 1-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Plasmid: PREST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19120

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Non-polymers , 5 types, 12 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: LiSO4, PEG 400, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 30, 2007 / Details: monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 32644 / Num. obs: 32644 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.15 / Χ2: 1.052 / Net I/σ(I): 7.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3071 / Rsym value: 0.551 / Χ2: 1.089 / % possible all: 92.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.23 Å42.38 Å
Translation3.23 Å42.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.115→42.375 Å / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1651 5.08 %random
Rwork0.224 ---
all0.227 33689 --
obs0.227 32490 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 7.8 Å2 / Biso mean: 53.44 Å2 / Biso min: 147.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.021 Å2-0 Å20 Å2
2---9.186 Å20 Å2
3---10.206 Å2
Refinement stepCycle: LAST / Resolution: 3.115→42.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9285 0 83 0 9368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129518
X-RAY DIFFRACTIONf_angle_d1.41912882
X-RAY DIFFRACTIONf_chiral_restr0.0911466
X-RAY DIFFRACTIONf_plane_restr0.0061669
X-RAY DIFFRACTIONf_dihedral_angle_d21.0153551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.115-3.2070.3231300.2892318244889.08
3.207-3.310.3091430.2662403254692.48
3.31-3.4290.311350.2492421255692.41
3.429-3.5660.2881400.242442258293.42
3.566-3.7280.2831450.2262538268396.2
3.728-3.9240.3011310.242583271498.08
3.924-4.170.3211330.2252618275198.57
4.17-4.4920.2731410.1962625276699.46
4.492-4.9430.2321180.1762682280099.26
4.943-5.6570.2611510.1992670282199.75
5.657-7.1220.2791310.2182720285199.89
7.122-42.3790.2231530.1862819297299.07

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