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- EMDB-20406: ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-20406
TitleClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4
Map data
Sample
  • Complex: ClpX-ClpP-substrate-ATPrS
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: substrate peptide
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsProtein degradation / AAA+ protease complex / CHAPERONE
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / endopeptidase Clp complex / endopeptidase Clp / 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 / serine-type peptidase activity ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / endopeptidase Clp / 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 / serine-type peptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / ATP-dependent protein folding chaperone / response to radiation / disordered domain specific binding / unfolded protein binding / protein folding / peptidase activity / ATPase binding / response to heat / protease binding / protein dimerization activity / cell division / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / ClpX zinc binding (ZB) domain profile. / ClpX C4-type zinc finger / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site ...Clp protease, ATP-binding subunit ClpX, bacteria / Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / 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 / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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 / 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: 4.2 Å
AuthorsFei X / Jenni S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-101988 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2020
Title: Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.
Authors: Xue Fei / Tristan A Bell / Simon Jenni / Benjamin M Stinson / Tania A Baker / Stephen C Harrison / Robert T Sauer /
Abstract: ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the ...ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.
History
DepositionJul 3, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseMar 11, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6po1
  • Surface level: 3.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6po1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20406.png

Downloads & links

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Map

FileDownload / File: emd_20406.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 3.01 / Movie #1: 3.01
Minimum - Maximum-9.798892 - 22.429414999999999
Average (Standard dev.)0.000000000007509 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z222.720222.720222.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-9.79922.4290.000

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Supplemental data

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Sample components

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Entire : ClpX-ClpP-substrate-ATPrS

EntireName: ClpX-ClpP-substrate-ATPrS
Components
  • Complex: ClpX-ClpP-substrate-ATPrS
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpX
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: substrate peptide
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ClpX-ClpP-substrate-ATPrS

SupramoleculeName: ClpX-ClpP-substrate-ATPrS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ER2566

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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: 39.835129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK ...String:
SALPTPHEIR NHLDDYVIGQ EQAKKVLAVA VYNHYKRLRN GDTSNGVELG KSNILLIGPT GSGKTLLAET LARLLDVPFT MADATTLTE AGYVGEDVEN IIQKLLQKSD YDVQKAQRGI VYIDQIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA A VPPQGGRK HPQQEFLQVD TSKILFICGG AFAGLDKVIS HRVETGSGIG FGATVKAKSD KASEGELLAQ VEPEDLIKFG LI PEFIGRL PVVATLNELS EEALIQILKE PKNALTKQYQ ALFNLEGVDL EFRDEALDAI AKKAMARKTG ARGLRSIVEA ALL DTMYDL PSMEDVEKVV IDESVIDGQS EPLLIYGKPE AQQASGEGGG TSG

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

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Macromolecule #2: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.21265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYSGERDNF APHMALVPMV IEQTSRGERS FDIYSRLLKE RVIFLTGQVE DHMANLIVAQ MLFLEAENPE KDIYLYINSP GGVITAGMS IYDTMQFIKP DVSTICMGQA ASMGAFLLTA GAKGKRFCLP NSRVMIHQPL GGYQGQATDI EIHAREILKV K GRMNELMA ...String:
MSYSGERDNF APHMALVPMV IEQTSRGERS FDIYSRLLKE RVIFLTGQVE DHMANLIVAQ MLFLEAENPE KDIYLYINSP GGVITAGMS IYDTMQFIKP DVSTICMGQA ASMGAFLLTA GAKGKRFCLP NSRVMIHQPL GGYQGQATDI EIHAREILKV K GRMNELMA LHTGQSLEQI ERDTERDRFL SAPEAVEYGL VDSILTHRN

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #3: substrate peptide

MacromoleculeName: substrate peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.039273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(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: 5 / 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: -2.5 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: -0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3mt6

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 227257
Details2X binned and motioncor2 corrected
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3hws

chain_id: A, source_name: PDB, initial_model_type: experimental model

3mt6

source_name: PDB, initial_model_type: experimental model
Output model

PDB-6po1:
ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4

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