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- EMDB-9028: Mtb ClpB in complex with AMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-9028
TitleMtb ClpB in complex with AMPPNP
Map data
Sample
  • Complex: Mtb ClpB in complex with AMPPNP
    • Protein or peptide: Chaperone protein ClpB
KeywordscryoEM / pathogen / AAA ATPase / Mycobacterium tuberculosis / unfoldase / CHAPERONE
Function / homology
Function and homology information


peptidoglycan-based cell wall / cellular response to heat / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / plasma membrane / 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 ...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 / Clp repeat (R) domain profile. / 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 / Chaperone protein ClpB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsYu HJ / Li HL
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: ATP hydrolysis-coupled peptide translocation mechanism of ClpB.
Authors: Hongjun Yu / Tania J Lupoli / Amanda Kovach / Xing Meng / Gongpu Zhao / Carl F Nathan / Huilin Li /
Abstract: The protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In (), ClpB facilitates asymmetric distribution ...The protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In (), ClpB facilitates asymmetric distribution of protein aggregates during cell division to help the pathogen survive and persist within the host, but a mechanistic understanding has been lacking. Here we report cryo-EM structures at 3.8- to 3.9-Å resolution of ClpB bound to a model substrate, casein, in the presence of the weakly hydrolyzable ATP mimic adenosine 5'-[γ-thio]triphosphate. ClpB existed in solution in two closed-ring conformations, conformers 1 and 2. In both conformers, the 12 pore-loops on the 12 NTDs of the six protomers (P1-P6) were arranged similarly to a staircase around the bound peptide. Conformer 1 is a low-affinity state in which three of the 12 pore-loops (the protomer P1 NBD1 and NBD2 loops and the protomer P2 NBD1 loop) are not engaged with peptide. Conformer 2 is a high-affinity state because only one pore-loop (the protomer P2 NBD1 loop) is not engaged with the peptide. The resolution of the two conformations, along with their bound substrate peptides and nucleotides, enabled us to propose a nucleotide-driven peptide translocation mechanism of a bacterial ClpB that is largely consistent with several recent unfoldase structures, in particular with the eukaryotic Hsp104. However, whereas Hsp104's two NBDs move in opposing directions during one step of peptide translocation, in Mtb ClpB the two NBDs move only in the direction of translocation.
History
Header (metadata) releaseJul 11, 2018-
DepositionAug 8, 2018-
Map releaseSep 26, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ed3
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9028.png

Downloads & links

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Map

FileDownload / File: emd_9028.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 292 pix.
= 313.608 Å		1.07 Å/pix.
x 292 pix.
= 313.608 Å		1.07 Å/pix.
x 292 pix.
= 313.608 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.022923049 - 0.07863158
Average (Standard dev.)0.00045267036 (±0.003384252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 313.608 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z292292292
origin x/y/z0.0000.0000.000
length x/y/z313.608313.608313.608
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS292292292
D min/max/mean-0.0230.0790.000

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Supplemental data

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Sample components

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Entire : Mtb ClpB in complex with AMPPNP

EntireName: Mtb ClpB in complex with AMPPNP
Components
  • Complex: Mtb ClpB in complex with AMPPNP
    • Protein or peptide: Chaperone protein ClpB

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Supramolecule #1: Mtb ClpB in complex with AMPPNP

SupramoleculeName: Mtb ClpB in complex with AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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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

UniProtKB: Chaperone protein ClpB

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 112043
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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