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- PDB-8d0i: Human SARM1 bound to an NB-3 eADPR adduct -

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Basic information

Entry
Database: PDB / ID: 8d0i
TitleHuman SARM1 bound to an NB-3 eADPR adduct
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-PZ7 / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBratkowski, M.A. / Mathur, P.
Funding support1items
OrganizationGrant numberCountry
Other private
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)34,0664
Polymers32,4112
Non-polymers1,6552
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.273, 78.797, 116.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
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-PZ7 / [[(2~{R},3~{S},4~{R},5~{R})-5-imidazo[2,1-f]purin-3-yl-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-[(1~{S})-1-[methyl-[2,2,2-tris(fluoranyl)ethylcarbamoyl]amino]ethyl]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 827.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H36F3N8O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.37 Å3/Da / Density % sol: 48 %
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: 8.3.1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→39.4 Å / Num. obs: 20965 / % possible obs: 97.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.927 / Rmerge(I) obs: 0.524 / Rpim(I) all: 0.209 / Rrim(I) all: 0.565 / Net I/σ(I): 4.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2066 / CC1/2: 0.826 / Rpim(I) all: 0.357 / Rrim(I) all: 0.957 / % possible all: 98.2

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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: 2→39.4 Å / SU ML: 0.201 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 2000 9.54 %
Rwork0.1735 18965 -
obs0.1777 20965 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.72 Å2
Refinement stepCycle: LAST / Resolution: 2→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 110 192 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732452
X-RAY DIFFRACTIONf_angle_d0.77653348
X-RAY DIFFRACTIONf_chiral_restr0.0528368
X-RAY DIFFRACTIONf_plane_restr0.005414
X-RAY DIFFRACTIONf_dihedral_angle_d20.4096870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27921420.20231347X-RAY DIFFRACTION98.35
2.05-2.110.21821390.18491313X-RAY DIFFRACTION96.16
2.11-2.170.24751410.17881342X-RAY DIFFRACTION98.47
2.17-2.240.26081330.18131253X-RAY DIFFRACTION90.71
2.24-2.320.28581420.17921357X-RAY DIFFRACTION100
2.32-2.410.24341420.17891336X-RAY DIFFRACTION96.92
2.41-2.520.21911470.18451394X-RAY DIFFRACTION100
2.52-2.650.22451390.18921334X-RAY DIFFRACTION97.68
2.65-2.820.23771370.18881293X-RAY DIFFRACTION93.04
2.82-3.040.24321450.18921374X-RAY DIFFRACTION97.56
3.04-3.340.26071470.17741388X-RAY DIFFRACTION99.22
3.34-3.820.18191460.15911391X-RAY DIFFRACTION99.35
3.82-4.820.15181440.13451360X-RAY DIFFRACTION94.59
4.82-39.40.19741560.18191483X-RAY DIFFRACTION97.27

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