9C88

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate

• PDB DOI: https://doi.org/10.2210/pdb9C88/pdb
• EM Map EMD-45300: EMDB EMDataResource

• Classification: CHAPERONE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 0.1288, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-12 Released: 2024-10-16 
• Deposition Author(s): Ghanbarpour, A., Sauer, R.T., Davis, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a fully-engaged DHFR-ssrA substrate and the AAA+ ClpXP protease

Ghanbarpour, A., Sauer, R.T., Davis, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 21-mer - A14B6C1 Local Symmetry: Dihedral - D7  (Explore in 3D)
Local Stoichiometry: Homo 14-mer - A14 

Local Symmetry: Dihedral - D7  (Explore in 3D)
Local Stoichiometry: Homo 14-mer - A14 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 586.47 kDa 
• Atom Count: 36,826 
• Modelled Residue Count: 4,733 
• Deposited Residue Count: 5,236 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-Degron DHFR	A [auth S]	10	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpX	B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	388	Escherichia coli	Mutation(s): 0  Gene Names: clpX, lopC, b0438, JW0428
UniProt
Find proteins for P0A6H1 (Escherichia coli (strain K12)) Explore P0A6H1  Go to UniProtKB:  P0A6H1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	207	Escherichia coli	Mutation(s): 0  Gene Names: clpP, lopP, b0437, JW0427 EC: 3.4.21.92
UniProt
Find proteins for P0A6G7 (Escherichia coli (strain K12)) Explore P0A6G7  Go to UniProtKB:  P0A6G7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	V [auth A], X [auth B], Z [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	BA [auth D], DA [auth E], EA [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	AA [auth C], CA [auth D], W [auth A], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Ghanbarpour, A., Sauer, R.T., Davis, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01-GM144542
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM141517
National Science Foundation (NSF, United States)	United States	2046778

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release