+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20845 | |||||||||
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Title | ClpA/ClpP Disengaged State bound to RepA-GFP | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process / serine-type peptidase activity ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation / ATPase binding / cellular response to heat / response to heat / response to oxidative stress / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Lopez KL / Rizo AR / Southworth DR | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis. Authors: Kyle E Lopez / Alexandrea N Rizo / Eric Tse / JiaBei Lin / Nathaniel W Scull / Aye C Thwin / Aaron L Lucius / James Shorter / Daniel R Southworth / Abstract: The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ...The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop-substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis. | |||||||||
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_20845.map.gz | 778.1 MB | EMDB map data format | |
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Header (meta data) | emd-20845-v30.xml emd-20845.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_20845.png | 134.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20845 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20845 | HTTPS FTP |
-Validation report
Summary document | emd_20845_validation.pdf.gz | 165 KB | Display | EMDB validaton report |
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Full document | emd_20845_full_validation.pdf.gz | 164.5 KB | Display | |
Data in XML | emd_20845_validation.xml.gz | 499 B | Display | |
Data in CIF | emd_20845_validation.cif.gz | 373 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20845 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20845 | HTTPS FTP |
-Related structure data
Related structure data | 6uqeMC 6uqoC 6w1zC 6w20C 6w21C 6w22C 6w23C 6w24C 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_20845.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.853 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 : ClpAP
Entire | Name: ClpAP |
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Components |
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-Supramolecule #1: ClpAP
Supramolecule | Name: ClpAP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 840 KDa |
-Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpA
Macromolecule | Name: ATP-dependent Clp protease ATP-binding subunit ClpA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 64.204504 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MENFTTNLNQ LARVGGIDPL IGREKELERA IQVLCRRRKN NPLLVGESGV GKTAIAEGLA WRIVQGDVPE VMADCTIYSL DIGSLLAGT KYRGDFEKRF KALLKQLEQD TNSILFIDEI HTIIGAGAAS GGQVDAANLI KPLLSSGKIR VIGSTTYQEF S NIFEKDRA ...String: MENFTTNLNQ LARVGGIDPL IGREKELERA IQVLCRRRKN NPLLVGESGV GKTAIAEGLA WRIVQGDVPE VMADCTIYSL DIGSLLAGT KYRGDFEKRF KALLKQLEQD TNSILFIDEI HTIIGAGAAS GGQVDAANLI KPLLSSGKIR VIGSTTYQEF S NIFEKDRA LARRFQKIDI TEPSIEETVQ IINGLKPKYE AHHDVRYTAK AVRAAVELAV KYINDRHLPD KAIDVIDEAG AR ARLMPVS KRKKTVNVAD IESVVARIAR IPEKSVSQSD RDTLKNLGDR LKMLVFGQDK AIEALTEAIK MARAGLGHEH KPV GSFLFA GPTGVGKTEV TVQLSKALGI ELLRFDMSEY MERHTVSRLI GAPPGYVGFD QGGLLTDAVI KHPHAVLLLD EIEK AHPDV FNILLQVMDN GTLTDNNGRK ADFRNVVLVM TTNAGVRETE RKSIGLIHQD NSTDAMEEIK KIFTPEFRNR LDNII WFDH LSTDVIHQVV DKFIVELQVQ LDQKGVSLEV SQEARNWLAE KGYDRAMGAR PMARVIQDNL KKPLANELLF GSLVDG GQV TVALDKEKNE LTYGF |
-Macromolecule #2: ATP-dependent Clp protease proteolytic subunit
Macromolecule | Name: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 21.472762 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: ALVPMVIEQT SRGERSFDIY SRLLKERVIF LTGQVEDHMA NLIVAQMLFL EAENPEKDIY LYINSPGGVI TAGMSIYDTM QFIKPDVST ICMGQAASMG AFLLTAGAKG KRFCLPNSRV MIHQPLGGYQ GQATDIEIHA REILKVKGRM NELMALHTGQ S LEQIERDT ...String: ALVPMVIEQT SRGERSFDIY SRLLKERVIF LTGQVEDHMA NLIVAQMLFL EAENPEKDIY LYINSPGGVI TAGMSIYDTM QFIKPDVST ICMGQAASMG AFLLTAGAKG KRFCLPNSRV MIHQPLGGYQ GQATDIEIHA REILKVKGRM NELMALHTGQ S LEQIERDT ERDRFLSAPE AVEYGLVDSI LTHR |
-Macromolecule #3: RepA-GFP
Macromolecule | Name: RepA-GFP / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 869.063 Da |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #4: RepA-GFP
Macromolecule | Name: RepA-GFP / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 954.168 Da |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 7 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-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 K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average exposure time: 6.0 sec. / Average electron dose: 69.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 58616 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 169000 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |