9RAI | pdb_00009rai

Structure of the S.aureus MecA/ClpC/ClpP degradation system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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Literature

Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP.

Azinas, S.Wallden, K.Katikaridis, P.Jenne, T.Schahl, A.Mogk, A.Carroni, M.

(2025) Commun Biol 8: 1467-1467

  • DOI: https://doi.org/10.1038/s42003-025-08908-w
  • Primary Citation of Related Structures:  
    9R2S, 9RAI

  • PubMed 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 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.


  • Organizational Affiliation
    • Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adapter protein MecA
A, B, C, D, E
A, B, C, D, E, F
239Staphylococcus aureusMutation(s): 0 
Gene Names: mecASAUSA300_0899
UniProt
Find proteins for Q2G1U5 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G1U5 
Go to UniProtKB:  Q2G1U5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G1U5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
unknown substrateG [auth S]18Staphylococcus aureusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpC818Staphylococcus aureusMutation(s): 0 
Gene Names: clpCSAOUHSC_00505
UniProt
Find proteins for Q2G0P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G0P5 
Go to UniProtKB:  Q2G0P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G0P5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit195Staphylococcus aureusMutation(s): 0 
Gene Names: clpPSAOUHSC_00790
EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G036 
Go to UniProtKB:  Q2G036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G036
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
CA [auth b]
FA [auth c]
GA [auth c]
JA [auth c]
KA [auth d]
CA [auth b],
FA [auth c],
GA [auth c],
JA [auth c],
KA [auth d],
OA [auth e]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth a],
DA [auth b],
NA [auth e],
RA [auth f]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
EA [auth b]
HA [auth c]
IA [auth c]
LA [auth d]
MA [auth d]
EA [auth b],
HA [auth c],
IA [auth c],
LA [auth d],
MA [auth d],
PA [auth e],
QA [auth e]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
MODEL REFINEMENTServalcat0.2.137
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references