9GI1 | pdb_00009gi1

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

PDB DOI: https://doi.org/10.2210/pdb9GI1/pdb
EM Map EMD-51367: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Staphylococcus aureus, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-16 Released: 2025-08-20
Deposition Author(s): Azinas, S., Wallden, K., Katikaridis, P., Schahl, A., Mogk, A., Carroni, M.
Funding Organization(s): Knut and Alice Wallenberg Foundation

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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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

ClpC and ClpP act as reciprocal allosteric activators to form a highly efficient AAA+ protease

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

To be published.

Macromolecule Content

Total Structure Weight: 855.95 kDa
Atom Count: 47,097
Modeled Residue Count: 6,024
Deposited Residue Count: 7,666
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A [auth Pa] B [auth Pb] C [auth Pc] D [auth Pd] E [auth Pe] A [auth Pa], B [auth Pb], C [auth Pc], D [auth Pd], E [auth Pe], F [auth Pf], G [auth Pg], H [auth Ph], I [auth Pi], J [auth Pl], K [auth Pm], L [auth Pn], M [auth Po], N [auth Pq]	195	Staphylococcus aureus	Mutation(s): 0 Gene Names: clpP, SAOUHSC_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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G036
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified substrate of the MecA-ClpC-ClpP complex from S.aureus	O [auth S]	28	Escherichia coli	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC	P [auth a] Q [auth b] R [auth c] S [auth d] T [auth e] P [auth a], Q [auth b], R [auth c], S [auth d], T [auth e], U [auth f]	818	Staphylococcus aureus	Mutation(s): 0 Gene Names: clpC, SAOUHSC_00505
UniProt
Find proteins for Q2G0P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0P5 Go to UniProtKB: Q2G0P5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G0P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain AA [auth c] SDF format, chain DA [auth d] SDF format, chain EA [auth d] SDF format, chain IA [auth e] SDF format, chain W [auth b] SDF format, chain Z [auth c] MOL2 format, chain AA [auth c] MOL2 format, chain DA [auth d] MOL2 format, chain EA [auth d] MOL2 format, chain IA [auth e] MOL2 format, chain W [auth b] MOL2 format, chain Z [auth c] mmCIF format, chain AA [auth c] mmCIF format, chain DA [auth d] mmCIF format, chain EA [auth d] mmCIF format, chain IA [auth e] mmCIF format, chain W [auth b] mmCIF format, chain Z [auth c]	AA [auth c] DA [auth d] EA [auth d] IA [auth e] W [auth b] AA [auth c], DA [auth d], EA [auth d], IA [auth e], W [auth b], Z [auth c]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain AA [auth c] Focus chain DA [auth d] Focus chain EA [auth d] Focus chain IA [auth e] Focus chain W [auth b] Focus chain Z [auth c] Interactions & Density Focus chain AA [auth c] Focus chain DA [auth d] Focus chain EA [auth d] Focus chain IA [auth e] Focus chain W [auth b] Focus chain Z [auth c]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain HA [auth e] SDF format, chain LA [auth f] SDF format, chain V [auth a] SDF format, chain X [auth b] MOL2 format, chain HA [auth e] MOL2 format, chain LA [auth f] MOL2 format, chain V [auth a] MOL2 format, chain X [auth b] mmCIF format, chain HA [auth e] mmCIF format, chain LA [auth f] mmCIF format, chain V [auth a] mmCIF format, chain X [auth b]	HA [auth e], LA [auth f], V [auth a], X [auth b]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain HA [auth e] Focus chain LA [auth f] Focus chain V [auth a] Focus chain X [auth b] Interactions & Density Focus chain HA [auth e] Focus chain LA [auth f] Focus chain V [auth a] Focus chain X [auth b]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth c] SDF format, chain CA [auth c] SDF format, chain FA [auth d] SDF format, chain GA [auth d] SDF format, chain JA [auth e] SDF format, chain KA [auth e] SDF format, chain Y [auth b] MOL2 format, chain BA [auth c] MOL2 format, chain CA [auth c] MOL2 format, chain FA [auth d] MOL2 format, chain GA [auth d] MOL2 format, chain JA [auth e] MOL2 format, chain KA [auth e] MOL2 format, chain Y [auth b] mmCIF format, chain BA [auth c] mmCIF format, chain CA [auth c] mmCIF format, chain FA [auth d] mmCIF format, chain GA [auth d] mmCIF format, chain JA [auth e] mmCIF format, chain KA [auth e] mmCIF format, chain Y [auth b]	BA [auth c] CA [auth c] FA [auth d] GA [auth d] JA [auth e] BA [auth c], CA [auth c], FA [auth d], GA [auth d], JA [auth e], KA [auth e], Y [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth c] Focus chain CA [auth c] Focus chain FA [auth d] Focus chain GA [auth d] Focus chain JA [auth e] Focus chain KA [auth e] Focus chain Y [auth b] Interactions & Density Focus chain BA [auth c] Focus chain CA [auth c] Focus chain FA [auth d] Focus chain GA [auth d] Focus chain JA [auth e] Focus chain KA [auth e] Focus chain Y [auth b]