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- PDB-9goq: Structure of the S.aureus MecA protein, in complex with ClpC -

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Basic information

Entry
Database: PDB / ID: 9goq
TitleStructure of the S.aureus MecA protein, in complex with ClpC
Components
  • ATP-dependent Clp protease ATP-binding subunit ClpC
  • Adapter protein MecA
KeywordsCHAPERONE / proteolysis / AAA+ adaptor protein / S.aureus
Function / homology
Function and homology information


peptidase activity / cellular response to heat / protein-macromolecule adaptor activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp repeat (R) N-terminal domain / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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
Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus (bacteria)
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCarroni, M. / Azinas, S.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2021.0347 Sweden
The Swedish Foundation for Strategic ResearchRIF21-0047 Sweden
CitationJournal: Commun Biol / Year: 2025
Title: Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP.
Authors: Stavros Azinas / Karin Wallden / Panagiotis Katikaridis / Timo Jenne / Adrien Schahl / Axel Mogk / Marta Carroni /
Abstract: Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are ...Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are crucial for stress resistance and virulence. ClpC requires cooperation with adaptor proteins such as MecA for activation and complex formation with ClpP. Here, we present the cryo-EM structure of the MecA/ClpC/ClpP complex from the major pathogen Staphylococcus aureus. MecA forms a dynamic crown on top of the ClpC/ClpP complex with its substrate-binding domain positioned near the ClpC pore site, likely facilitating substrate transfer. ClpC/ClpP complex formation involves ClpC P-loops and ClpP N-terminal β-hairpins, which insert into the central ClpC threading channel and contact sites next to the ClpC ATPase center. ClpC and ClpP interactions are asymmetric and dictated by the activity states of ClpC ATPase subunits. ClpP binding increases ClpC ATPase and threading activities in a β-hairpin dependent manner, illuminating an allosteric pathway in the cooperation of ATPase and peptidase components in bacterial AAA+ proteases.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adapter protein MecA
a: ATP-dependent Clp protease ATP-binding subunit ClpC
B: Adapter protein MecA
C: Adapter protein MecA
D: Adapter protein MecA
E: Adapter protein MecA
F: Adapter protein MecA
b: ATP-dependent Clp protease ATP-binding subunit ClpC
c: ATP-dependent Clp protease ATP-binding subunit ClpC
d: ATP-dependent Clp protease ATP-binding subunit ClpC
e: ATP-dependent Clp protease ATP-binding subunit ClpC
f: ATP-dependent Clp protease ATP-binding subunit ClpC
g: ATP-dependent Clp protease ATP-binding subunit ClpC
h: ATP-dependent Clp protease ATP-binding subunit ClpC
i: ATP-dependent Clp protease ATP-binding subunit ClpC
l: ATP-dependent Clp protease ATP-binding subunit ClpC
m: ATP-dependent Clp protease ATP-binding subunit ClpC
n: ATP-dependent Clp protease ATP-binding subunit ClpC


Theoretical massNumber of molelcules
Total (without water)1,264,16918
Polymers1,264,16918
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Adapter protein MecA


Mass: 28354.170 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus (bacteria)
Gene: mecA, EP54_04625, EQ90_04635, FAF17_07790, GO814_05005, GO942_02320, GQX37_01765, HMPREF3211_01912, NCTC10702_01523, NCTC13131_00648, SAMEA2078260_00478, SAMEA2078588_00142, SAMEA2080344_00168, ...Gene: mecA, EP54_04625, EQ90_04635, FAF17_07790, GO814_05005, GO942_02320, GQX37_01765, HMPREF3211_01912, NCTC10702_01523, NCTC13131_00648, SAMEA2078260_00478, SAMEA2078588_00142, SAMEA2080344_00168, SAMEA2081063_00168, SAMEA4008575_00168, SAMEA70146418_02921
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A0D3Q6A0
#2: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC / Endopeptidase Clp ATP-binding subunit C / Hemolysin B


Mass: 91170.352 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: clpC, BER48_000499, CEJ93_12415, ERS072738_00457, ERS072840_00763, ERS073583_01020, ERS074020_00452, HMPREF3211_01370
Production host: Escherichia coli (E. coli) / References: UniProt: W8U1E4
Has protein modificationN

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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: N-terminal part of the complex between the AAA+ unfoldase ClpC and the adaptor protein MecA from S.aureus.
Type: COMPLEX
Details: This is referred in the paper as the MecA crown and includes only the N-terminal and coiled-coil part of ClpC.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 24000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82800 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 174.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007514106
ELECTRON MICROSCOPYf_angle_d0.820119056
ELECTRON MICROSCOPYf_chiral_restr0.05362148
ELECTRON MICROSCOPYf_plane_restr0.00852478
ELECTRON MICROSCOPYf_dihedral_angle_d13.86945286

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