8SU9

E. coli SIR2-HerA complex (hexamer HerA bound with dodecamer Sir2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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

Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense.

Shen, Z.Lin, Q.Yang, X.Y.Fosuah, E.Fu, T.M.

(2023) Mol Cell 83: 4586-4599.e5

  • DOI: https://doi.org/10.1016/j.molcel.2023.11.007
  • Primary Citation of Related Structures:  
    8SU9, 8SUB, 8SUW, 8SXX, 8UAE, 8UAF

  • PubMed Abstract: 

    SIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD + upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex reveals a dynamic assembly process. Unlike other ATPases, HerA can form various oligomers, ranging from dimers to nonamers. When assembled with SIR2, HerA forms a hexamer and converts SIR2 from a nuclease to an NAD + hydrolase, representing an unexpected regulatory mechanism mediated by protein assembly. Furthermore, high concentrations of ATP can inhibit NAD + hydrolysis by the SIR2-HerA complex. Cryo-EM structures of the SIR2-HerA complex reveal a giant supramolecular assembly up to 1 MDa, with SIR2 as a dodecamer and HerA as a hexamer, crucial for anti-phage defense. Unexpectedly, the HerA hexamer resembles a spiral staircase and exhibits helicase activities toward dual-forked DNA. Together, we reveal the supramolecular assembly of SIR2-HerA as a unique mechanism for switching enzymatic activities and bolstering anti-phage defense strategies.


  • Organizational Affiliation

    Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIR2-like domain-containing protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
415Escherichia coliMutation(s): 0 
Gene Names: ERS139208_00135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside triphosphate hydrolase
M, N, O, P, Q
M, N, O, P, Q, R
610Escherichia coliMutation(s): 0 
Gene Names: ERS139208_00134
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
S [auth A]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
S [auth A],
T [auth B],
U [auth C],
V [auth D],
W [auth E],
X [auth F],
Y [auth G],
Z [auth H]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
EA [auth M],
GA [auth N],
IA [auth O],
KA [auth P],
MA [auth Q]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
FA [auth M],
HA [auth N],
JA [auth O],
LA [auth P],
NA [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release