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- EMDB-49274: Cryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-49274
TitleCryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex from Pseudomonas aeruginosa bound to the AAA+ ClpX unfoldase.
Map data
Sample
  • Complex: ClpX
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: Unknown substrate
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsClpXP / full-engaged state / AAA protease / CHAPERONE
Function / homology
Function and homology information


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 / protein dimerization 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 / protein dimerization activity / serine-type endopeptidase activity / cell division / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / : / 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 / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / : / 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 proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit ClpX / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsGhanbarpour A / Zhang JJ / Baker TA / Davis JH / Sauer RT
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of ClpX from Pseudomonas aeruginosa
Authors: Ghanbarpour A / Sauer RT / Davis JH
History
DepositionFeb 18, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49274.png

Downloads & links

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Map

FileDownload / File: emd_49274.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.
= 287.77 Å		1.12 Å/pix.
x 256 pix.
= 287.77 Å		1.12 Å/pix.
x 256 pix.
= 287.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1241 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0571
Minimum - Maximum-0.25078794 - 0.5882912
Average (Standard dev.)0.002040065 (±0.024585726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 287.7696 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49274_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49274_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_49274_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 : ClpX

EntireName: ClpX
Components
  • Complex: ClpX
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: Unknown substrate
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ClpX

SupramoleculeName: ClpX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 47.049688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDTRNGEDN GKLLYCSFCG KSQHEVRKLI AGPSVFICDE CVDLCNDIIR EEVQEAQAES SGHKLPAPKE IRTILDQYVI GQERAKKVL AVAVYNHYKR LNQRDKKDDI ELGKSNILMI GPTGSGKTLL AETLARLLNV PFTIADATTL TEAGYVGEDV E NIIQKLLQ ...String:
MTDTRNGEDN GKLLYCSFCG KSQHEVRKLI AGPSVFICDE CVDLCNDIIR EEVQEAQAES SGHKLPAPKE IRTILDQYVI GQERAKKVL AVAVYNHYKR LNQRDKKDDI ELGKSNILMI GPTGSGKTLL AETLARLLNV PFTIADATTL TEAGYVGEDV E NIIQKLLQ KCDYDVEKAQ MGIVYIDEID KISRKSDNPS ITRDVSGEGV QQALLKLIEG TVASVPPQGG RKHPQQEFLQ VD TRNILFI CGGAFAGLER VIQNRSARGG IGFNAEVRSQ EMGKKVGEAF KEVEPEDLVK FGLIPEFVGR LPVIATLDEL DEA ALMQIL TEPKNALTKQ YAKLFEMEGV DLEFRPDALK AVARKALERK TGARGLRSIL EGILLDTMYE IPSQQDVSKV VIDE SVIDG SSQPLMIYEN SEKPAKAAPE A

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

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Macromolecule #2: Unknown substrate

MacromoleculeName: Unknown substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 443.539 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)

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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: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 23.529143 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MSRNSFIPHV PDIQAAGGLV PMVVEQSARG ERAYDIYSRL LKERIIFLVG QVEDYMANLV VAQLLFLEAE NPEKDIHLYI NSPGGSVTA GMSIYDTMQF IKPNVSTTCI GQACSMGALL LAGGAAGKRY CLPHSRMMIH QPLGGFQGQA SDIEIHAKEI L FIKERLNQ ...String:
MSRNSFIPHV PDIQAAGGLV PMVVEQSARG ERAYDIYSRL LKERIIFLVG QVEDYMANLV VAQLLFLEAE NPEKDIHLYI NSPGGSVTA GMSIYDTMQF IKPNVSTTCI GQACSMGALL LAGGAAGKRY CLPHSRMMIH QPLGGFQGQA SDIEIHAKEI L FIKERLNQ ILAHHTGQPL DVIARDTDRD RFMSGDEAVK YGLIDKVMTQ RDLAV

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #4: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 23.167191 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MKTDDKDREG GDSHGAIGAK LMEYALKVRK VFVTGGVDEK MAKDVVQQLH ILASISDDPI YMFVNSPGGH VESGDMIFDA IRFITPKVI MIGSGSVASA GALIYAAADK ENRYSLPNTR FLLHQPSGGI QGPASNIEIY RREIVRMKER LDRIFAEATG Q TPEKISAD ...String:
MKTDDKDREG GDSHGAIGAK LMEYALKVRK VFVTGGVDEK MAKDVVQQLH ILASISDDPI YMFVNSPGGH VESGDMIFDA IRFITPKVI MIGSGSVASA GALIYAAADK ENRYSLPNTR FLLHQPSGGI QGPASNIEIY RREIVRMKER LDRIFAEATG Q TPEKISAD TERDFWLNAE EAVQYGLVNK IIVSEREITL PGQDYKDDDD K

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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 BIOQUANTUM (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 / 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 correctionDetails: Patch CTF estimation, cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135056
Initial angle assignmentType: PROJECTION MATCHING / Details: Ab-initio reconstruction, cryoSPARC
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

SoftwareName: cryoSPARC (ver. 4.4.1)
Output model

PDB-9ndj:
Cryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex from Pseudomonas aeruginosa bound to the AAA+ ClpX unfoldase.

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