6ZFX | pdb_00006zfx

hSARM1 GraFix-ed


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6ZFX

This is version 1.4 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7ANW

Literature

Structural basis for SARM1 inhibition and activation under energetic stress.

Sporny, M.Guez-Haddad, J.Khazma, T.Yaron, A.Dessau, M.Shkolnisky, Y.Mim, C.Isupov, M.N.Zalk, R.Hons, M.Opatowsky, Y.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.62021
  • Primary Citation Related Structures: 
    6ZFX, 6ZG0, 6ZG1, 7ANW

  • PubMed Abstract: 

    SARM1, an executor of axonal degeneration, displays NADase activity that depletes the key cellular metabolite, NAD+, in response to nerve injury. The basis of SARM1 inhibition and its activation under stress conditions are still unknown. Here, we present cryo-EM maps of SARM1 at 2.9 and 2.7 Å resolutions. These indicate that SARM1 homo-octamer avoids premature activation by assuming a packed conformation, with ordered inner and peripheral rings, that prevents dimerization and activation of the catalytic domains. This inactive conformation is stabilized by binding of SARM1's own substrate NAD+ in an allosteric location, away from the catalytic sites. This model was validated by mutagenesis of the allosteric site, which led to constitutively active SARM1. We propose that the reduction of cellular NAD+ concentration contributes to the disassembly of SARM1's peripheral ring, which allows formation of active NADase domain dimers, thereby further depleting NAD+ to cause an energetic catastrophe and cell death.


  • Organizational Affiliation
    • The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

Macromolecule Content 

  • Total Structure Weight: 642.46 kDa 
  • Atom Count: 39,856 
  • Modeled Residue Count: 5,080 
  • Deposited Residue Count: 5,808 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD(+) hydrolase SARM1
A, B, C, D, E
A, B, C, D, E, F, G, H
726Homo sapiensMutation(s): 1 
Gene Names: SARM1KIAA0524SAMD2SARM
EC: 3.2.2.6 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SZW1 (Homo sapiens)
Explore Q6SZW1 
Go to UniProtKB:  Q6SZW1
PHAROS:  Q6SZW1
GTEx:  ENSG00000004139 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6SZW1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S1N

Query on S1N



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth H]
(~{E})-4-methylnon-4-enedial
C10 H16 O2
AFKSPUYAXUNQPA-UXBLZVDNSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1425/15
Israel Science FoundationIsrael909/19

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2022-11-09
    Changes: Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary