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- PDB-9hqh: SARM1 TIR domain in complex with compound 28-ADPR -

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Basic information

Entry
Database: PDB / ID: 9hqh
TitleSARM1 TIR domain in complex with compound 28-ADPR
ComponentsNAD(+) hydrolase SARM1
KeywordsHYDROLASE / NAD / AXONAL DEGENERATION
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 / synapse / dendrite / glutamatergic 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
: / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsGiroud, M. / Kuhn, B. / Steiner, S. / Westwood, P. / Mendel, M. / Mani, A. / Pinard, E. / Haap, W. / Grether, U. / Caramenti, P. ...Giroud, M. / Kuhn, B. / Steiner, S. / Westwood, P. / Mendel, M. / Mani, A. / Pinard, E. / Haap, W. / Grether, U. / Caramenti, P. / Rombach, D. / Zambaldo, C. / Ritter, M. / Schmid, P. / Gasser, C. / Aregger, N. / Sechet, N. / Topp, A. / Bilyard, M. / Malnight-Alvarez, A. / Plitzko, I. / Hilbert, M. / Kalayil, S. / Burger, D. / Bonardi, C. / Saal, W. / Haider, A. / Wittwer, M. / Brigo, A. / Keaney, J. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARM1 TIR domain in complex with compounds
Authors: Giroud, M. / Kuhn, B. / Steiner, S. / Westwood, P. / Mendel, M. / Mani, A. / Pinard, E. / Haap, W. / Grether, U. / Caramenti, P. / Rombach, D. / Zambaldo, C. / Ritter, M. / Schmid, P. / ...Authors: Giroud, M. / Kuhn, B. / Steiner, S. / Westwood, P. / Mendel, M. / Mani, A. / Pinard, E. / Haap, W. / Grether, U. / Caramenti, P. / Rombach, D. / Zambaldo, C. / Ritter, M. / Schmid, P. / Gasser, C. / Aregger, N. / Sechet, N. / Topp, A. / Bilyard, M. / Malnight-Alvarez, A. / Plitzko, I. / Hilbert, M. / Kalayil, S. / Burger, D. / Bonardi, C. / Saal, W. / Haider, A. / Wittwer, M. / Brigo, A. / Keaney, J. / Benz, J.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(+) hydrolase SARM1
B: NAD(+) hydrolase SARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9414
Polymers33,1022
Non-polymers1,8392
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area13450 Å2
Unit cell
Length a, b, c (Å)33.146, 78.014, 115.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 16550.887 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-A1IWN / [[(2~{S},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-[(1~{R})-1-[[(3~{R})-4,4-bis(fluoranyl)oxolan-3-yl]carbamoyl-methyl-amino]-2-phenoxy-ethyl]pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 919.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H43F2N8O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 6.5, 14-18% (w/v) PEG 3350 and 0.30-0.45 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.988→64.718 Å / Num. obs: 14405 / % possible obs: 90.5 % / Redundancy: 6.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.24 / Net I/σ(I): 5.6
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 0.718 / Num. unique obs: 200 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.988→64.718 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.566 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24058 768 5.3 %RANDOM
Rwork0.19727 ---
obs0.19953 13630 66.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2---0.41 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.988→64.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 124 109 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162317
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.8073408
X-RAY DIFFRACTIONr_angle_other_deg0.5671.8045371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1855294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.68358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87410424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022825
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02553
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4031.4181150
X-RAY DIFFRACTIONr_mcbond_other1.4021.4181151
X-RAY DIFFRACTIONr_mcangle_it2.3892.5371439
X-RAY DIFFRACTIONr_mcangle_other2.3892.5361440
X-RAY DIFFRACTIONr_scbond_it2.1011.6781344
X-RAY DIFFRACTIONr_scbond_other2.11.6781345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5232.9851965
X-RAY DIFFRACTIONr_long_range_B_refined4.88615.762806
X-RAY DIFFRACTIONr_long_range_B_other4.88215.522801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.04 Å
RfactorNum. reflection% reflection
Rfree0.407 3 -
Rwork0.295 25 -
obs--1.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2216-0.10950.10140.1145-0.04860.1556-0.0099-0.0081-0.01-0.0068-0.0067-0.0007-0.01350.00910.01660.0035-0.00020.00010.0393-0.00090.00577.8733-2.7194-3.8827
20.34920.06820.07770.06340.06860.0890.0039-0.0085-0.01230.0030.00090.0031-0.0072-0.0063-0.00490.00860.00150.00570.01950.00420.005111.0377-7.531-32.1207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A561 - 803
2X-RAY DIFFRACTION2B561 - 801

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