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- PDB-6o1b: Crystal structure of the TIR domain G601P mutant from human SARM1... -

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Basic information

Entry
Database: PDB / ID: 6o1b
TitleCrystal structure of the TIR domain G601P mutant from human SARM1, crystal form 1
ComponentsSterile alpha and TIR motif-containing protein 1
KeywordsSIGNALING PROTEIN / 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 / 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
NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHorsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. ...Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. / Rank, M. / Casey, L. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
Funding support Australia, 6items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1107804 Australia
National Health and Medical Research Council (NHMRC, Australia)1160570 Australia
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1108859 Australia
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
CitationJournal: Science / Year: 2019
Title: NAD+cleavage activity by animal and plant TIR domains in cell death pathways.
Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. ...Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
History
DepositionFeb 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5692
Polymers16,3741
Non-polymers1951
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.737, 54.138, 74.912
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 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: 16373.768 Da / Num. of mol.: 1 / Mutation: G601P
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
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 MES pH 6.0, 0.2 M MgCl2, 20% PEG3350; or 0.1 MES pH 6.0, 1 M LiCl, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.67→43.88 Å / Num. obs: 16080 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 792 / CC1/2: 0.976 / Rpim(I) all: 0.111 / Rrim(I) all: 0.295 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→30.802 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1604 10 %
Rwork0.185 --
obs0.1896 16032 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→30.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 12 131 1260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141172
X-RAY DIFFRACTIONf_angle_d1.2221589
X-RAY DIFFRACTIONf_dihedral_angle_d17.913439
X-RAY DIFFRACTIONf_chiral_restr0.08174
X-RAY DIFFRACTIONf_plane_restr0.01201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6702-1.72410.27761420.22551282X-RAY DIFFRACTION99
1.7241-1.78570.22971420.2141275X-RAY DIFFRACTION100
1.7857-1.85720.2361440.19941298X-RAY DIFFRACTION100
1.8572-1.94170.24981430.19841286X-RAY DIFFRACTION100
1.9417-2.04410.24431450.18961311X-RAY DIFFRACTION100
2.0441-2.17210.24651430.19311285X-RAY DIFFRACTION100
2.1721-2.33980.2011470.17541318X-RAY DIFFRACTION100
2.3398-2.57510.22751460.18331314X-RAY DIFFRACTION100
2.5751-2.94750.21791460.18651309X-RAY DIFFRACTION100
2.9475-3.71260.2261490.17451342X-RAY DIFFRACTION100
3.7126-30.80770.23621570.18041408X-RAY DIFFRACTION99

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