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- EMDB-71688: Cryo-EM structure of the ClpXP AAA+ protease bound to an unidenti... -

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Basic information

Entry
Database: EMDB / ID: EMD-71688
TitleCryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex
Map data
Sample
  • Complex: ClpXP complex bound to an unidentified portion of Lambda O-ARC within a translocation complex.
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • RNA: unidentified portion of the substrate
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsAAA+ protease / ClpXP / substrate-bound / CHAPERONE
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 / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process ...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 / proteasomal protein catabolic process / serine-type peptidase activity / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / peptidase activity / response to heat / ATPase binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / ClpP, Ser active site / Endopeptidase Clp serine active site. ...Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / : / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ClpP/crotonase-like domain superfamily / 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
ATP-dependent Clp protease ATP-binding subunit ClpX / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsGhanbarpour A / Davis JH / Sauer RT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc within a translocation complex
Authors: Ghanbarpour A / Davis JH / Sauer RT
History
DepositionJul 13, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71688.png

Downloads & links

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Map

FileDownload / File: emd_71688.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 256 pix.
= 287.744 Å		1.12 Å/pix.
x 256 pix.
= 287.744 Å		1.12 Å/pix.
x 256 pix.
= 287.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0465
Minimum - Maximum-0.37517253 - 0.8002831
Average (Standard dev.)0.00009413754 (±0.028575454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 287.744 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71688_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71688_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71688_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ClpXP complex bound to an unidentified portion of Lambda O-ARC wi...

EntireName: ClpXP complex bound to an unidentified portion of Lambda O-ARC within a translocation complex.
Components
  • Complex: ClpXP complex bound to an unidentified portion of Lambda O-ARC within a translocation complex.
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • RNA: unidentified portion of the substrate
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ClpXP complex bound to an unidentified portion of Lambda O-ARC wi...

SupramoleculeName: ClpXP complex bound to an unidentified portion of Lambda O-ARC within a translocation complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit ClpX

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpX / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.414848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVAPHRE RSALPTPHEI RNHLDDYVIG QEQAKKVLA VAVYNHYKRL RNGDTSNGVE LGKSNILLIG PTGSGKTLLA ETLARLLDVP FTMADATTLT EAGYVGEDVE N IIQKLLQK ...String:
MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVAPHRE RSALPTPHEI RNHLDDYVIG QEQAKKVLA VAVYNHYKRL RNGDTSNGVE LGKSNILLIG PTGSGKTLLA ETLARLLDVP FTMADATTLT EAGYVGEDVE N IIQKLLQK CDYDVQKAQR GIVYIDEIDK ISRKSDNPSI TRDVSGEGVQ QALLKLIEGT VAAVPPQGGR KHPQQEFLQV DT SKILFIC GGAFAGLDKV ISHRVETGSG IGFGATVKAK SDKASEGELL AQVEPEDLIK FGLIPEFIGR LPVVATLNEL SEE ALIQIL KEPKNALTKQ YQALFNLEGV DLEFRDEALD AIAKKAMARK TGARGLRSIV EAALLDTMYD LPSMEDVEKV VIDE SVIDG QSEPLLIYGK PEAQQASGE

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpX

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Macromolecule #3: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: 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: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.468869 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LVPMVIEQTS RGERSFDIYS RLLKERVIFL TGQVEDHMAN LIVAQMLFLE AENPEKDIYL YINSPGGVIT AGMSIYDTMQ FIKPDVSTI CMGQAASMGA FLLTAGAKGK RFCLPNSRVM IHQPLGGYQG QATDIEIHAR EILKVKGRMN ELMALHTGQS L EQIERDTE ...String:
LVPMVIEQTS RGERSFDIYS RLLKERVIFL TGQVEDHMAN LIVAQMLFLE AENPEKDIYL YINSPGGVIT AGMSIYDTMQ FIKPDVSTI CMGQAASMGA FLLTAGAKGK RFCLPNSRVM IHQPLGGYQG QATDIEIHAR EILKVKGRMN ELMALHTGQS L EQIERDTE RDRFLSAPEA VEYGLVDSIL THRNENLYFQ SLEHHHHHH

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #2: unidentified portion of the substrate

MacromoleculeName: unidentified portion of the substrate / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 465.671 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 6 / 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 #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 52.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Ab-initio reconstruction, cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 325578
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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