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- PDB-8d0f: Human SARM1 TIR domain bound to NB-2-ADPR -

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Basic information

Entry
Database: PDB / ID: 8d0f
TitleHuman SARM1 TIR domain bound to NB-2-ADPR
ComponentsNAD(+) hydrolase SARM1
KeywordsHYDROLASE/INHIBITOR / NAD / hydrolase / axon degeneration / neuroscience / HYDROLASE-INHIBITOR complex
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 / NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / nervous system process ...negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to axon injury / response to glucose / 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 / nervous system development / mitochondrial outer membrane / microtubule / cell differentiation / axon / innate immune response / dendrite / synapse / cell surface / signal transduction / protein-containing complex / 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-Q0U / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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)33,9904
Polymers32,4112
Non-polymers1,5792
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.940, 86.363, 115.757
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
11B-973-

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-Q0U / [[(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})-5-[4-[[methyl-[2,2,2-tris(fluoranyl)ethylcarbamoyl]amino]methyl]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 789.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H34F3N8O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
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: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.74→48.08 Å / Num. obs: 34455 / % possible obs: 99 % / Redundancy: 13 % / Biso Wilson estimate: 19.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.04 / Rrim(I) all: 0.147 / Net I/σ(I): 13
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 1.364 / Mean I/σ(I) obs: 13 / Num. unique obs: 3371 / CC1/2: 0.776 / Rpim(I) all: 0.415 / Rrim(I) all: 1.482

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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: 1.74→48.08 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 2000 5.8 %
Rwork0.2126 32455 -
obs0.215 34455 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.11 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 104 166 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612409
X-RAY DIFFRACTIONf_angle_d0.92743279
X-RAY DIFFRACTIONf_chiral_restr0.0566361
X-RAY DIFFRACTIONf_plane_restr0.0054404
X-RAY DIFFRACTIONf_dihedral_angle_d16.9572306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.33921400.29792272X-RAY DIFFRACTION99.71
1.78-1.830.34151390.26912241X-RAY DIFFRACTION95.89
1.83-1.890.29921390.26632262X-RAY DIFFRACTION100
1.89-1.950.29321380.24282254X-RAY DIFFRACTION96.76
1.95-2.020.28081430.23682308X-RAY DIFFRACTION99.92
2.02-2.10.27351390.21742255X-RAY DIFFRACTION97.59
2.1-2.190.26711420.21622308X-RAY DIFFRACTION98.35
2.19-2.310.22941420.21442300X-RAY DIFFRACTION99.59
2.31-2.450.29141400.21762286X-RAY DIFFRACTION98.74
2.45-2.640.32231440.22812326X-RAY DIFFRACTION99.08
2.64-2.910.27061450.22122341X-RAY DIFFRACTION99.48
2.91-3.330.24461450.21332370X-RAY DIFFRACTION99.33
3.33-4.190.21691480.18432401X-RAY DIFFRACTION99.77
4.19-48.080.20341560.18842531X-RAY DIFFRACTION99.74

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