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 8TRG | pdb_00008trg

Structure of full-length LexA bound to a RecA filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8TRG

This is version 1.3 of the entry. See complete history. 

Literature

The LexA-RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation.

Cory, M.B., Li, A., Hurley, C.M., Carman, P.J., Pumroy, R.A., Hostetler, Z.M., Perez, R.M., Venkatesh, Y., Li, X., Gupta, K., Petersson, E.J., Kohli, R.M.

(2024) Nat Struct Mol Biol 31: 1522-1531

  • DOI: https://doi.org/10.1038/s41594-024-01317-3
  • Primary Citation Related Structures: 
    8TRG

  • PubMed Abstract: 

    The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.


  • Organizational Affiliation: 
    • Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 387.18 kDa 
  • Atom Count: 22,866 
  • Modeled Residue Count: 2,941 
  • Deposited Residue Count: 3,469 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein RecA
A, B, C, D, E
A, B, C, D, E, F, G, H
379Escherichia coliMutation(s): 0 
Gene Names: recA
UniProt
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Explore P0A7G6 
Go to UniProtKB:  P0A7G6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7G6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LexA repressor
I, J
205Escherichia coliMutation(s): 1 
Gene Names: lexA
EC: 3.4.21.88
UniProt
Find proteins for P0A7C2 (Escherichia coli (strain K12))
Explore P0A7C2 
Go to UniProtKB:  P0A7C2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7C2
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (27-MER)K [auth L]27Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS

Query on AGS



Download:Ideal Coordinates CCD File
L [auth A]
N [auth B]
P [auth C]
R [auth D]
T [auth E]
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth H]
M [auth A]
O [auth B]
Q [auth C]
S [auth D]
AA [auth H],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTISOLDE1.4
RECONSTRUCTIONcryoSPARC4.0.3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM127593

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary