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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0376 | |||||||||
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Title | Hsp104DWB open conformation | |||||||||
![]() | Hsp104DWB in open conformation, primary map | |||||||||
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![]() | Hsp104 / ClpB / protein disaggregase / molecular chaperone / AAA+ / ATPase / cryo-EM / CHAPERONE | |||||||||
Function / homology | ![]() 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 / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.3 Å | |||||||||
![]() | Lee S / Rho SH | |||||||||
![]() | ![]() Title: Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation. Authors: Sukyeong Lee / Soung Hun Roh / Jungsoon Lee / Nuri Sung / Jun Liu / Francis T F Tsai / ![]() Abstract: Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with ...Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with Clp/Hsp100 protein unfoldases, different and seemingly conflicting 3D structures have been reported. Examining the structure of Hsp104 poses considerable challenges because Hsp104 readily hydrolyzes ATP, whereas ATP analogs can be slowly turned over and are often contaminated with other nucleotide species. Here, we present the single-particle electron cryo-microscopy (cryo-EM) structures of a catalytically inactive Hsp104 variant (Hsp104) in the ATP-bound state determined between 7.7 Å and 9.3 Å resolution. Surprisingly, we observe that the Hsp104 hexamer adopts distinct ring conformations (closed, extended, and open) despite being in the same nucleotide state. The latter underscores the structural plasticity of Hsp104 in solution, with different conformations stabilized by nucleotide binding. Our findings suggest that, in addition to ATP hydrolysis-driven conformational changes, Hsp104 uses stochastic motions to translocate unfolded polypeptides. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12 KB 12 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.6 KB | Display | ![]() |
Images | ![]() | 55.9 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n8vMC ![]() 0375C ![]() 0377C ![]() 6n8tC ![]() 6n8zC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Hsp104DWB in open conformation, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Hexamer of Hsp104 with ATP
Entire | Name: Hexamer of Hsp104 with ATP |
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Components |
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-Supramolecule #1: Hexamer of Hsp104 with ATP
Supramolecule | Name: Hexamer of Hsp104 with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Hsp 104 double Walker B mutant |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: Heat shock protein 104
Macromolecule | Name: Heat shock protein 104 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 99.046859 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QFTERALTIL TLAQKLASDH QHPQLQPIHI LAAFIETPED GSVPYLQNLI EKGRYDYDLF KKVVNRNLVR IPQQQPAPAE ITPSYALGK VLQDAAKIQK QQKDSFIAQD HILFALFNDS SIQQIFKEAQ VDIEAIKQQA LELRGNTRID SRGADTNTPL E YLSKYAID ...String: QFTERALTIL TLAQKLASDH QHPQLQPIHI LAAFIETPED GSVPYLQNLI EKGRYDYDLF KKVVNRNLVR IPQQQPAPAE ITPSYALGK VLQDAAKIQK QQKDSFIAQD HILFALFNDS SIQQIFKEAQ VDIEAIKQQA LELRGNTRID SRGADTNTPL E YLSKYAID MTEQARQGKL DPVIGREEEI RSTIRVLARR IKSNPCLIGE PGIGKTAIIE GVAQRIIDDD VPTILQGAKL FS LDLAALT AGAKYKGDFE ERFKGVLKEI EESKTLIVLF IDEIHMLMGN GKDDAANILK PALSRGQLKV IGATTNNEYR SIV EKDGAF ERRFQKIEVA EPSVRQTVAI LRGLQPKYEI HHGVRILDSA LVTAAQLAKR YLPYRRLPDS ALDLVDISCA GVAV ARDSK PEELDSKERQ LQLIQVEIKA LERDEDADST TKDRLKLARQ KEASLQEELE PLRQRYNEEK HGHEELTQAK KKLDE LENK ALDAERRYDT ATAADLRYFA IPDIKKQIEK LEDQVAEEER RAGANSMIQN VVDSDTISET AARLTGIPVK KLSESE NEK LIHMERDLSS EVVGQMDAIK AVSNAVRLSR SGLANPRQPA SFLFLGLSGS GKTELAKKVA GFLFNDEDMM IRVDCSE LS EKYAVSKLLG TTAGYVGYDE GGFLTNQLQY KPYSVLLFDE VEKAHPDVLT VMLQMLDDGR ITSGQGKTID CSNCIVIM T SNLGAEFINS QQGSKIQEST KNLVMGAVRQ HFRPEFLNRI SSIVIFNKLS RKAIHKIVDI RLKEIEERFE QNDKHYKLN LTQEAKDFLA KYGYSDDMGA RPLNRLIQNE ILNKLALRIL KNEIKDKETV NVVLKKGKSR DENVPEEAEE CLEVLPNHE UniProtKB: Heat shock protein 104 |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 11 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Buffer solution is freshly prepared. | ||||||||||||
Grid | Details: unspecified | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging. | ||||||||||||
Details | This sample was mono disperse. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1394 / Average exposure time: 7.6 sec. / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |