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- PDB-8d0e: Human SARM1 TIR domain bound to NB-7 -

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Basic information

Entry
Database: PDB / ID: 8d0e
TitleHuman SARM1 TIR domain bound to NB-7
ComponentsNAD(+) hydrolase SARM1
KeywordsHYDROLASE/INHIBITOR / NAD / hydrolase / axon degeneration / neuroscience / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


extrinsic component of synaptic membrane / negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / NADP+ nucleosidase activity / Toll Like Receptor 3 (TLR3) Cascade / NAD+ catabolic process / NAD+ nucleosidase activity / regulation of synapse pruning / modification of postsynaptic structure / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...extrinsic component of synaptic membrane / negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / NADP+ nucleosidase activity / Toll Like Receptor 3 (TLR3) Cascade / NAD+ catabolic process / NAD+ nucleosidase activity / regulation of synapse pruning / modification of postsynaptic structure / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleosidase activity, cyclic ADP-ribose generating / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to glucose / response to axon injury / regulation of neuron apoptotic process / signaling adaptor activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / neuromuscular junction / nervous system development / microtubule / mitochondrial outer membrane / cell differentiation / axon / innate immune response / dendrite / synapse / glutamatergic synapse / cell surface / signal transduction / protein-containing complex / mitochondrion / identical protein binding / cytoplasm / cytosol
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-Q0C / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBratkowski, M.A. / Mathur, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Neuron / Year: 2022
Title: Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease.
Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / ...Authors: Bratkowski, M. / Burdett, T.C. / Danao, J. / Wang, X. / Mathur, P. / Gu, W. / Beckstead, J.A. / Talreja, S. / Yang, Y.S. / Danko, G. / Park, J.H. / Walton, M. / Brown, S.P. / Tegley, C.M. / Joseph, P.R.B. / Reynolds, C.H. / Sambashivan, S.
History
DepositionMay 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 25, 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: NAD(+) hydrolase SARM1
B: NAD(+) hydrolase SARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0934
Polymers32,4112
Non-polymers6822
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-7 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.927, 87.232, 116.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1098-

HOH

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Components

#1: Protein NAD(+) hydrolase SARM1 / NADase SARM1 / hSARM1 / NADP(+) hydrolase SARM1 / Sterile alpha and Armadillo repeat protein / ...NADase SARM1 / hSARM1 / NADP(+) hydrolase SARM1 / Sterile alpha and Armadillo repeat protein / Sterile alpha and TIR motif-containing protein 1 / Sterile alpha motif domain-containing protein 2 / MyD88-5 / SAM domain-containing protein 2 / Tir-1 homolog / HsTIR


Mass: 16205.574 Da / Num. of mol.: 2 / Fragment: TIR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARM1, KIAA0524, SAMD2, SARM / Production host: Escherichia coli (E. coli)
References: UniProt: Q6SZW1, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-Q0C / 3-(4-chlorophenyl)-N-[4-methyl-3-(pyridin-4-yl)-1H-pyrazol-5-yl]propanamide


Mass: 340.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17ClN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris propane pH 6.5, 200 mM potassium thiocyanate, and 15% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.88→48.48 Å / Num. obs: 28243 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 26.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.041 / Rrim(I) all: 0.143 / Net I/σ(I): 12.2
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2807 / CC1/2: 0.809 / Rpim(I) all: 0.359 / Rrim(I) all: 1.298 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D0J

8d0j


Resolution: 1.88→48.48 Å / SU ML: 0.1668 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 1998 7.07 %
Rwork0.1831 26245 -
obs0.1862 28243 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 1.88→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 48 215 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632381
X-RAY DIFFRACTIONf_angle_d0.84783230
X-RAY DIFFRACTIONf_chiral_restr0.0582350
X-RAY DIFFRACTIONf_plane_restr0.0058415
X-RAY DIFFRACTIONf_dihedral_angle_d7.1734310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.27511400.25771847X-RAY DIFFRACTION99.95
1.93-1.980.25921410.21481835X-RAY DIFFRACTION99.95
1.98-2.040.2591380.20431834X-RAY DIFFRACTION99.9
2.04-2.10.26211400.18791844X-RAY DIFFRACTION99.95
2.1-2.180.22141420.18141848X-RAY DIFFRACTION100
2.18-2.270.26121380.19521831X-RAY DIFFRACTION99.95
2.27-2.370.25931440.1771884X-RAY DIFFRACTION99.8
2.37-2.490.21871400.18231840X-RAY DIFFRACTION99.95
2.49-2.650.20891410.18521858X-RAY DIFFRACTION100
2.65-2.850.23251440.18991872X-RAY DIFFRACTION99.95
2.85-3.140.23821430.191882X-RAY DIFFRACTION99.9
3.14-3.60.23811450.18121906X-RAY DIFFRACTION100
3.6-4.530.21291470.15751922X-RAY DIFFRACTION99.95
4.53-48.480.19741550.18272042X-RAY DIFFRACTION99.95

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