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- EMDB-21557: Cryo-EM map of the Mycobacterium tuberculosis ClpB disaggregase h... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21557 | |||||||||
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Title | Cryo-EM map of the Mycobacterium tuberculosis ClpB disaggregase hexamer with a locally refined N-terminal domain in the presence of DnaK chaperone and a model substrate | |||||||||
![]() | Conformation T with NTD | |||||||||
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![]() | ClpB-DnaK complex / protein aggregates / Refold / Unfold / CHAPERONE | |||||||||
Function / homology | ![]() protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / Resolution: 3.2 Å | |||||||||
![]() | Yin Y / Li H | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. Authors: Yanting Yin / Xiang Feng / Hongjun Yu / Allison Fay / Amanda Kovach / Michael S Glickman / Huilin Li / ![]() Abstract: The M. tuberculosis (Mtb) ClpB is a protein disaggregase that helps to rejuvenate the bacterial cell. DnaK is a protein foldase that can function alone, but it can also bind to the ClpB hexamer to ...The M. tuberculosis (Mtb) ClpB is a protein disaggregase that helps to rejuvenate the bacterial cell. DnaK is a protein foldase that can function alone, but it can also bind to the ClpB hexamer to physically couple protein disaggregation with protein refolding, although the molecular mechanism is not well understood. Here, we report the cryo-EM analysis of the Mtb ClpB-DnaK bi-chaperone in the presence of ATPγS and a protein substrate. We observe three ClpB conformations in the presence of DnaK, identify a conserved TGIP loop linking the oligonucleotide/oligosaccharide-binding domain and the nucleotide-binding domain that is important for ClpB function, derive the interface between the regulatory middle domain of the ClpB and the DnaK nucleotide-binding domain, and find that DnaK binding stabilizes, but does not bend or tilt, the ClpB middle domain. We propose a model for the synergistic actions of aggregate dissolution and refolding by the Mtb ClpB-DnaK bi-chaperone system. | |||||||||
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 | ![]() | 164.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.2 KB 12.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 106.9 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w6jMC ![]() 6w6eC ![]() 6w6gC ![]() 6w6hC ![]() 6w6iC ![]() 7l6nC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Conformation T with NTD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 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 : ClpB/DnaK complex
Entire | Name: ClpB/DnaK complex |
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Components |
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-Supramolecule #1: ClpB/DnaK complex
Supramolecule | Name: ClpB/DnaK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Chaperone protein ClpB
Macromolecule | Name: Chaperone protein ClpB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 92.688281 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDSFNPTTKT QAALTAALQA ASTAGNPEIR PAHLLMALLT QNDGIAAPLL EAVGVEPATV RAETQRLLDR LPQATGASTQ PQLSRESLA AITTAQQLAT ELDDEYVSTE HVMVGLATGD SDVAKLLTGH GASPQALREA FVKVRGSARV TSPEPEATYQ A LQKYSTDL ...String: MDSFNPTTKT QAALTAALQA ASTAGNPEIR PAHLLMALLT QNDGIAAPLL EAVGVEPATV RAETQRLLDR LPQATGASTQ PQLSRESLA AITTAQQLAT ELDDEYVSTE HVMVGLATGD SDVAKLLTGH GASPQALREA FVKVRGSARV TSPEPEATYQ A LQKYSTDL TARAREGKLD PVIGRDNEIR RVVQVLSRRT KNNPVLIGEP GVGKTAIVEG LAQRIVAGDV PESLRDKTIV AL DLGSMVA GSKYRGEFEE RLKAVLDDIK NSAGQIITFI DELHTIVGAG ATGEGAMDAG NMIKPMLARG ELRLVGATTL DEY RKHIEK DAALERRFQQ VYVGEPSVED TIGILRGLKD RYEVHHGVRI TDSALVAAAT LSDRYITARF LPDKAIDLVD EAAS RLRME IDSRPVEIDE VERLVRRLEI EEMALSKEED EASAERLAKL RSELADQKEK LAELTTRWQN EKNAIEIVRD LKEQL EALR GESERAERDG DLAKAAELRY GRIPEVEKKL DAALPQAQAR EQVMLKEEVG PDDIADVVSA WTGIPAGRLL EGETAK LLR MEDELGKRVI GQKAAVTAVS DAVRRSRAGV SDPNRPTGAF MFLGPTGVGK TELAKALADF LFDDERAMVR IDMSEYG EK HTVARLIGAP PGYVGYEAGG QLTEAVRRRP YTVVLFDEIE KAHPDVFDVL LQVLDEGRLT DGHGRTVDFR NTILILTS N LGSGGSAEQV LAAVRATFKP EFINRLDDVL IFEGLNPEEL VRIVDIQLAQ LGKRLAQRRL QLQVSLPAKR WLAQRGFDP VYGARPLRRL VQQAIGDQLA KMLLAGQVHD GDTVPVNVSP DADSLILG UniProtKB: Chaperone protein ClpB |
-Macromolecule #2: Substrate
Macromolecule | Name: Substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.486056 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 10 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
![]() | single particle reconstruction |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |