+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7943 | |||||||||
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Title | Mtb ClpB in complex with ATPgammaS and casein, Conformer 2 | |||||||||
Map data | Mtb ClpB in complex with ATPgammaS and casein, Conformer 2 | |||||||||
Sample |
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Keywords | cryoEM / pathogen / AAA ATPase / Mycobacterium tuberculosis / unfoldase / CHAPERONE | |||||||||
Function / homology | Function and homology information protein unfolding / peptidoglycan-based cell wall / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Yu HJ / Li HL | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7943.map.gz | 88.8 MB | EMDB map data format | |
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Header (meta data) | emd-7943-v30.xml emd-7943.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7943_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_7943.png | 56.2 KB | ||
Filedesc metadata | emd-7943.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7943 | HTTPS FTP |
-Validation report
Summary document | emd_7943_validation.pdf.gz | 631.1 KB | Display | EMDB validaton report |
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Full document | emd_7943_full_validation.pdf.gz | 630.7 KB | Display | |
Data in XML | emd_7943_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_7943_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7943 | HTTPS FTP |
-Related structure data
Related structure data | 6djvMC 7942C 9027C 9028C 6djuC 6ed3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7943.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mtb ClpB in complex with ATPgammaS and casein, Conformer 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Mtb ClpB in complex with ATPgammaS and casein
Entire | Name: Mtb ClpB in complex with ATPgammaS and casein |
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Components |
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-Supramolecule #1: Mtb ClpB in complex with ATPgammaS and casein
Supramolecule | Name: Mtb ClpB in complex with ATPgammaS and casein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
-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: Mycobacterium tuberculosis (bacteria) |
Molecular weight | Theoretical: 92.688281 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: casein polyAlanine model
Macromolecule | Name: casein polyAlanine model / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 1.866038 KDa |
Sequence | String: AAAAAAAAAA AAAAAAAAAA AAAAAA |
-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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |