+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-21187 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | ClpXP from Neisseria meningitidis - Conformation A | ||||||||||||
![]() | ClpXP from N. meningitidis - Conformation A | ||||||||||||
![]() |
| ||||||||||||
![]() | Complex / AAA+ / protease / ClpP / ClpX / HYDROLASE | ||||||||||||
Function / homology | ![]() HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / ATPase binding / peptidase activity ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / ATPase binding / peptidase activity / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Ripstein ZA / Vahidi S | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery. Authors: Zev A Ripstein / Siavash Vahidi / Walid A Houry / John L Rubinstein / Lewis E Kay / ![]() Abstract: The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ...The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here, we present cryo-EM structures of the substrate-bound ClpXP complex from at 2.3 to 3.3 Å resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 97.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
Images | ![]() | 55.1 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vfsMC ![]() 6vfxC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ClpXP from N. meningitidis - Conformation A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : ClpXP complex
Entire | Name: ClpXP complex |
---|---|
Components |
|
-Supramolecule #1: ClpXP complex
Supramolecule | Name: ClpXP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Complex formed between ClpX hexmers and a ClpP tetradecamer |
---|---|
Molecular weight | Theoretical: 860 KDa |
-Supramolecule #2: ATP-dependent Clp protease ATP-binding subunit ClpX, ATP-dependen...
Supramolecule | Name: ATP-dependent Clp protease ATP-binding subunit ClpX, ATP-dependent Clp protease proteolytic subunit type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3 |
---|---|
Source (natural) | Organism: ![]() |
-Supramolecule #3: Un-identified protein substrate
Supramolecule | Name: Un-identified protein substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpX
Macromolecule | Name: ATP-dependent Clp protease ATP-binding subunit ClpX / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.139438 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSNENRTCSF CGKSKSHVKH LIEGENAFIC DECVSNCIEI LHEDGNDGTP SESAGGEPEE SGKLPTPAEI VANLNDHVIG QEQAKKALA VSVYNHYKRL RHPKAGANVE LSKSNILLIG PTGSGKTLLA QSLARKLDVP FVMADATTLT EAGYVGEDVE Q IITKLLGK ...String: MSNENRTCSF CGKSKSHVKH LIEGENAFIC DECVSNCIEI LHEDGNDGTP SESAGGEPEE SGKLPTPAEI VANLNDHVIG QEQAKKALA VSVYNHYKRL RHPKAGANVE LSKSNILLIG PTGSGKTLLA QSLARKLDVP FVMADATTLT EAGYVGEDVE Q IITKLLGK CDFDVEKAQR GIVYIDQIDK ISRKSDNPSI TRDVSGEGVQ QALLKLIEGT VASVPPQGGR KHPNQEFINV DT TNILFIC GGAFAGLEKV IRQRTEKGGI GFGASVHSKD ENADITKLFG IVEPEDLIKF GLIPELIGRL PVIATLEILD EDA LINILT EPKNALVKQY QALFGMENVE LEFEEGALRS IARQAMERKT GARGLRSIVE RCLLDTMYRL PDLKGLKKVV VGKA VIEEG REPELVFES UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpX |
-Macromolecule #2: Unidentified protein substrate
Macromolecule | Name: Unidentified protein substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 613.749 Da |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: ATP-dependent Clp protease proteolytic subunit
Macromolecule | Name: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.729967 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSFDNYLVPT VIEQSGRGER AFDIYSRLLK ERIVFLVGPV TDESANLVVA QLLFLESENP DKDIFFYINS PGGSVTAGMS IYDTMNFIK PDVSTLCLGQ AASMGAFLLS AGEKGKRFAL PNSRIMIHQP LISGGLGGQA SDIEIHAREL LKIKEKLNRL M AKHCDRDL ...String: MSFDNYLVPT VIEQSGRGER AFDIYSRLLK ERIVFLVGPV TDESANLVVA QLLFLESENP DKDIFFYINS PGGSVTAGMS IYDTMNFIK PDVSTLCLGQ AASMGAFLLS AGEKGKRFAL PNSRIMIHQP LISGGLGGQA SDIEIHAREL LKIKEKLNRL M AKHCDRDL ADLERDTDRD NFMSAEEAKE YGLIDQILEN RASLRL UniProtKB: ATP-dependent Clp protease proteolytic subunit |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2 mg/mL | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8.5 Component:
Details: Buffer pH was measured as 8.2 at room temperature corresponding to a pH of 8.5 at 4 degrees, the temperature at which the complex was held before vitrification | ||||||||||
Grid | Model: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Details: Home-made gold grids were inspected before use | ||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: Blotted for 15 seconds at an offset of -5 mm. | ||||||||||
Details | Mono-disperse complexes |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Temperature | Min: 70.0 K / Max: 77.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2680 / Average exposure time: 60.0 sec. / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |