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- EMDB-21554: Cryo-EM map of the Mycobacterium tuberculosis ClpB disaggregase h... -

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Basic information

Entry
Database: EMDB / ID: EMD-21554
TitleCryo-EM map of the Mycobacterium tuberculosis ClpB disaggregase hexamer in conformation I in the presence of DnaK chaperone and a model substrate
Map dataConformation I
Sample
  • Complex: ClpB complex with Dnak
    • Protein or peptide: Chaperone protein ClpB
    • Protein or peptide: Substrate
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


response to heat / protein refolding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Chaperonin ClpB / 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 ...Chaperonin ClpB / 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
Chaperone protein ClpB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / Resolution: 3.1 Å
AuthorsYin Y / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH) United States
CitationJournal: Cell Rep / Year: 2021
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
DepositionMar 16, 2020-
Header (metadata) releaseApr 15, 2020-
Map releaseMar 17, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w6g
  • Surface level: 0.0194
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21554.png

Downloads & links

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Map

FileDownload / File: emd_21554.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConformation I
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.0136 / Movie #1: 0.0194
Minimum - Maximum-0.050330114 - 0.13301931
Average (Standard dev.)0.00017707677 (±0.0028930064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z386.640386.640386.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0500.1330.000

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Supplemental data

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Sample components

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Entire : ClpB complex with Dnak

EntireName: ClpB complex with Dnak
Components
  • Complex: ClpB complex with Dnak
    • Protein or peptide: Chaperone protein ClpB
    • Protein or peptide: Substrate
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ClpB complex with Dnak

SupramoleculeName: ClpB complex with Dnak / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Chaperone protein ClpB

MacromoleculeName: Chaperone protein ClpB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 92.688281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Substrate

MacromoleculeName: Substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 2.826475 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(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) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 10 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162924
FSC plot (resolution estimation)

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