9C87

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


Literature

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX

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

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpX
A, B, C, D, E
A, B, C, D, E, F
389Escherichia coliMutation(s): 0 
Gene Names: clpX, lopC, b0438, JW0428
UniProt
Find proteins for P0A6H1 (Escherichia coli (strain K12))
Explore P0A6H1 
Go to UniProtKB:  P0A6H1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6H1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductaseG [auth S]210Escherichia coliMutation(s): 0 
Gene Names: folA, HmCmsJML131_03510
EC: 1.5.1.3
UniProt
Find proteins for A0A4C7B7M9 (Escherichia coli)
Explore A0A4C7B7M9 
Go to UniProtKB:  A0A4C7B7M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4C7B7M9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit207Escherichia coliMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6G7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
Download Ideal Coordinates CCD File 
V [auth A],
X [auth B],
Z [auth C]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MTX (Subject of Investigation/LOI)
Query on MTX
Download Ideal Coordinates CCD File 
FA [auth S]METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
ADP (Subject of Investigation/LOI)
Query on ADP
Download Ideal Coordinates CCD File 
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)
Query on MG
Download Ideal Coordinates CCD File 
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: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14_3260:

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01-GM144542
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM141517
National Science Foundation (NSF, United States)United States2046778

Revision History  (Full details and data files)

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