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- PDB-7uiz: ClpAP complex bound to ClpS N-terminal extension, class IIc -

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Basic information

Entry
Database: PDB / ID: 7uiz
TitleClpAP complex bound to ClpS N-terminal extension, class IIc
Components(ATP-dependent Clp protease ...) x 3
KeywordsCHAPERONE / AAA+ protease / Adaptor / protein complex
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity ...endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
ATP-dependent Clp protease adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. ...ATP-dependent Clp protease adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / ClpA/B family / 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 family associated with various cellular activities (AAA) / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease adapter protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsKim, S. / Fei, X. / Sauer, R.T. / Baker, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: AAA+ protease-adaptor structures reveal altered conformations and ring specialization.
Authors: Sora Kim / Xue Fei / Robert T Sauer / Tania A Baker /
Abstract: ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore ...ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.
#1: Journal: To Be Published
Title: ClpAP AAA+ Protease Adaptor Structures Reveal Pore-Loop Specialization
Authors: Kim, S. / Fei, X. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpA
B: ATP-dependent Clp protease ATP-binding subunit ClpA
C: ATP-dependent Clp protease ATP-binding subunit ClpA
D: ATP-dependent Clp protease ATP-binding subunit ClpA
E: ATP-dependent Clp protease ATP-binding subunit ClpA
F: ATP-dependent Clp protease ATP-binding subunit ClpA
S: ATP-dependent Clp protease adapter protein ClpS
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)682,79836
Polymers676,56414
Non-polymers6,23422
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP-dependent Clp protease ... , 3 types, 14 molecules ABCDEFSHIJKLMN

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpA


Mass: 84291.758 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpA, AB05_1038 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A836NDF2
#2: Protein ATP-dependent Clp protease adapter protein ClpS


Mass: 12193.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpS, ECVG_02246 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3JJM5
#3: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22660.018 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K4NM46, endopeptidase Clp

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Non-polymers , 3 types, 22 molecules

#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AAA+ protease complex ClpAP bound to adaptor protein ClpS and GFP
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
4CTFFINDCTF correction
7PHENIXmodel fitting
8UCSF Chimeramodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
13RELIONfinal Euler assignment
14RELIONclassification
15PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38131 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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