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- PDB-7nah: Crystal structure of the TIR domain from human SARM1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nah
TitleCrystal structure of the TIR domain from human SARM1 in complex with 2AD
ComponentsSterile alpha and TIR motif-containing protein 1
KeywordsHYDROLASE / NADase / Axon degeneration
Function / homology
Function and homology information


negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / nervous system process ...negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to axon injury / response to glucose / signaling adaptor activity / regulation of neuron apoptotic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / nervous system development / microtubule / mitochondrial outer membrane / cell differentiation / axon / innate immune response / dendrite / synapse / signal transduction / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sterile alpha and TIR motif-containing protein 1 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Sterile alpha and TIR motif-containing protein 1 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Chem-1OF / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsShi, Y. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
CitationJournal: Mol Cell / Year: 2022
Title: Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules.
Authors: Yun Shi / Philip S Kerry / Jeffrey D Nanson / Todd Bosanac / Yo Sasaki / Raul Krauss / Forhad K Saikot / Sarah E Adams / Tamim Mosaiab / Veronika Masic / Xianrong Mao / Faith Rose / Eduardo ...Authors: Yun Shi / Philip S Kerry / Jeffrey D Nanson / Todd Bosanac / Yo Sasaki / Raul Krauss / Forhad K Saikot / Sarah E Adams / Tamim Mosaiab / Veronika Masic / Xianrong Mao / Faith Rose / Eduardo Vasquez / Marieke Furrer / Katie Cunnea / Andrew Brearley / Weixi Gu / Zhenyao Luo / Lou Brillault / Michael J Landsberg / Aaron DiAntonio / Bostjan Kobe / Jeffrey Milbrandt / Robert O Hughes / Thomas Ve /
Abstract: The NADase SARM1 (sterile alpha and TIR motif containing 1) is a key executioner of axon degeneration and a therapeutic target for several neurodegenerative conditions. We show that a potent SARM1 ...The NADase SARM1 (sterile alpha and TIR motif containing 1) is a key executioner of axon degeneration and a therapeutic target for several neurodegenerative conditions. We show that a potent SARM1 inhibitor undergoes base exchange with the nicotinamide moiety of nicotinamide adenine dinucleotide (NAD) to produce the bona fide inhibitor 1AD. We report structures of SARM1 in complex with 1AD, NAD mimetics and the allosteric activator nicotinamide mononucleotide (NMN). NMN binding triggers reorientation of the armadillo repeat (ARM) domains, which disrupts ARM:TIR interactions and leads to formation of a two-stranded TIR domain assembly. The active site spans two molecules in these assemblies, explaining the requirement of TIR domain self-association for NADase activity and axon degeneration. Our results reveal the mechanisms of SARM1 activation and substrate binding, providing rational avenues for the design of new therapeutics targeting SARM1.
History
DepositionJun 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterile alpha and TIR motif-containing protein 1
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0444
Polymers32,6672
Non-polymers1,3772
Water3,639202
1
A: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0222
Polymers16,3341
Non-polymers6881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0222
Polymers16,3341
Non-polymers6881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.235, 116.569, 32.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-993-

HOH

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Components

#1: Protein Sterile alpha and TIR motif-containing protein 1 / Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM ...Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM domain-containing protein 2 / Tir-1 homolog


Mass: 16333.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARM1, KIAA0524, SAMD2, SARM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6SZW1
#2: Chemical ChemComp-1OF / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(8-oxidanylidene-7~{H}-2,7-naphthyridin-2-yl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 688.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane pH 7.0, 0.2 M potassium thiocyanate, and 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→48.29 Å / Num. obs: 32174 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1854 / CC1/2: 0.944 / Rpim(I) all: 0.169 / Rrim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O0R

6o0r


Resolution: 1.79→43.12 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 2000 6.23 %
Rwork0.1683 30116 -
obs0.1702 32116 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.94 Å2
Refinement stepCycle: LAST / Resolution: 1.79→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 92 202 2538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012440
X-RAY DIFFRACTIONf_angle_d1.07413330
X-RAY DIFFRACTIONf_chiral_restr0.0606368
X-RAY DIFFRACTIONf_plane_restr0.0086472
X-RAY DIFFRACTIONf_dihedral_angle_d10.2384946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.31581390.27242088X-RAY DIFFRACTION98.06
1.84-1.890.23431380.21872089X-RAY DIFFRACTION100
1.89-1.940.21631420.17552136X-RAY DIFFRACTION100
1.94-20.22011390.15442092X-RAY DIFFRACTION100
2-2.080.17331410.14052122X-RAY DIFFRACTION100
2.08-2.160.18851420.15422140X-RAY DIFFRACTION100
2.16-2.260.19491410.17142120X-RAY DIFFRACTION99.96
2.26-2.380.22991420.18942146X-RAY DIFFRACTION100
2.38-2.520.20131440.15022156X-RAY DIFFRACTION100
2.52-2.720.20551420.15852137X-RAY DIFFRACTION100
2.72-2.990.18821440.16032177X-RAY DIFFRACTION100
2.99-3.430.19521440.15782166X-RAY DIFFRACTION100
3.43-4.320.17151470.14912212X-RAY DIFFRACTION99.96
4.32-43.120.2011550.18972335X-RAY DIFFRACTION99.92

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