5VYA | pdb_00005vya

S. cerevisiae Hsp104:casein complex, Extended Conformation

• PDB DOI: https://doi.org/10.2210/pdb5VYA/pdb
• EM Map EMD-8746: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae S288C, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-24 Released: 2017-07-05 
• Deposition Author(s): Gates, S.N., Yokom, A.L., Lin, J.-B., Jackrel, M.E., Rizo, A.N., Kendsersky, N.M., Buell, C.E., Sweeny, E.A., Chuang, E., Torrente, M.P., Mack, K.L., Su, M., Shorter, J., Southworth, D.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104.

Gates, S.N., Yokom, A.L., Lin, J., Jackrel, M.E., Rizo, A.N., Kendsersky, N.M., Buell, C.E., Sweeny, E.A., Mack, K.L., Chuang, E., Torrente, M.P., Su, M., Shorter, J., Southworth, D.R.

(2017) Science 357: 273-279

• PubMed: 28619716 
• DOI: https://doi.org/10.1126/science.aan1052
• Primary Citation Related Structures: 
  5VJH, 5VY8, 5VY9, 5VYA


• PubMed Abstract: 
  

  Hsp100 polypeptide translocases are conserved members of the AAA+ family (adenosine triphosphatases associated with diverse cellular activities) that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from Saccharomyces cerevisiae solubilizes stress-induced amorphous aggregates and amyloids. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo-electron microscopy structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80-angstrom-long unfolded polypeptide along the axial channel. Two protomers undergo a ratchet-like conformational change that advances pore loop-substrate interactions by two amino acids. These changes are coupled to activation of specific nucleotide hydrolysis sites and, when transmitted around the hexamer, reveal a processive rotary translocation mechanism and substrate-responsive flexibility during Hsp104-catalyzed disaggregation.

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Organizational Affiliation: 
• Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
Graduate Program in Chemical Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Chemistry Department of Brooklyn College and Ph.D. Programs in Chemistry, Biochemistry, and Biology, Graduate Center of the City University of New York, New York, NY 10016, USA.
Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 621.72 kDa 
• Atom Count: 27,691 
• Modeled Residue Count: 3,502 
• Deposited Residue Count: 5,476 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 104	A, B, C, D, E, F	908	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HSP104, YLL026W, L0948
UniProt
Find proteins for P31539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31539  Go to UniProtKB:  P31539

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-S1-casein	G [auth P]	28	Bos taurus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth E]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	G [auth P]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): Gates, S.N., Yokom, A.L., Lin, J.-B., Jackrel, M.E., Rizo, A.N., Kendsersky, N.M., Buell, C.E., Sweeny, E.A., Chuang, E., Torrente, M.P., Mack, K.L., Su, M., Shorter, J., Southworth, D.R.

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 2.0: 2017-07-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2017-08-02
  Changes: Database references
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary