6QWV

SARM1 SAM1-2 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Evidence for an Octameric Ring Arrangement of SARM1.

Sporny, M.Guez-Haddad, J.Lebendiker, M.Ulisse, V.Volf, A.Mim, C.Isupov, M.N.Opatowsky, Y.

(2019) J.Mol.Biol. 431: 3591-3605

  • DOI: 10.1016/j.jmb.2019.06.030

  • PubMed Abstract: 
  • SARM1 induces axonal degeneration in response to various insults, and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the inte ...

    SARM1 induces axonal degeneration in response to various insults, and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the integrity of the protein's SAM domains, as well as on the enzymatic conversion of NAD+ to ADPR (ADP Ribose) products by the SARM1's TIR domain. Therefore, inhibition of either SAM or TIR functions may constitute an effective therapeutic strategy. However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. In this study we found that SARM1 assembles into an octameric ring. This arrangement was not described before in other SAM proteins, but is reminiscent of the apoptosome and inflammasome - well known apoptotic ring-like oligomers. We show that both SARM1 and the isolated tandem SAM 1-2 domains form octamers in solution, and electron microscopy analysis reveals an octameric ring of SARM1. We determined the crystal structure of SAM 1-2 , and found that it also forms a closed octameric ring in the crystal lattice. The SAM 1-2 ring interactions are mediated by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between the neighboring protomers. We have mutated several interacting SAM 1-2 interfaces and measured how these mutations affect SARM1 apoptotic activity in cultured cells, and in this way identified critical oligomerization sites that facilitate cell death. These results highlight the importance of oligomerization for SARM1 function and reveal critical epitopes for future targeted drug development.


    Organizational Affiliation

    The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel. Electronic address: yarden.opatowsky@biu.ac.il.,Royal Technical Institute (KTH), Dept. For Biomedical Engineering and Health Solutions, Stockholm, Sweden; Karolinska Institute, Dept. of Nutrition and Biosciences, Huddinge, Sweden.,Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Israel.,Biosciences, University of Exeter, England.,The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.,Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sterile alpha and TIR motif-containing protein 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
164Homo sapiensMutation(s): 0 
Gene Names: SARM1 (KIAA0524, SAMD2, SARM)
EC: 3.2.2.6
Find proteins for Q6SZW1 (Homo sapiens)
Go to Gene View: SARM1
Go to UniProtKB:  Q6SZW1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, I, J, K, L, M, N, O, P
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
B, P
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B, D, J, K
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 252.246α = 90.00
b = 252.246β = 90.00
c = 49.766γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
CRANK2phasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael182/10
Israel Science FoundationIsrael1425/15

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Database references
  • Version 1.3: 2019-09-18
    Type: Data collection, Database references