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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 / Clp repeat (R) domain profile. / 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: To Be Published
Title: ClpC and ClpP act as reciprocal allosteric activators to form a highly efficient AAA+ protease
Authors: Azinas, S. / Wallden, K. / Katikaridis, P. / Schahl, A. / Mogk, A. / Carroni, M.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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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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