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- PDB-6o0r: Crystal structure of the TIR domain from human SARM1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6o0r
TitleCrystal structure of the TIR domain from human SARM1 in complex with glycerol
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 / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / nervous system process ...negative regulation of MyD88-independent toll-like receptor signaling pathway / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to axon injury / response to glucose / signaling adaptor activity / regulation of neuron apoptotic process / 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 / microtubule / mitochondrial outer membrane / cell differentiation / axon / innate immune response / dendrite / synapse / signal transduction / 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: 1.8 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. / Deerain, N. / 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 17, 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

Downloads & links

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Assembly

Deposited unit
A: Sterile alpha and TIR motif-containing protein 1
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8524
Polymers32,6672
Non-polymers1842
Water3,513195
1
A: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4262
Polymers16,3341
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4262
Polymers16,3341
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.056, 86.127, 116.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 16333.703 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis Tris propane pH 6.5, 0.2 M potassium thiocyanate, 11% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→48.33 Å / Num. obs: 31910 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.081 / Rrim(I) all: 0.22 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.435 / Mean I/σ(I) obs: 1 / Num. unique obs: 1902 / CC1/2: 0.285 / Rpim(I) all: 0.963 / Rrim(I) all: 2.621 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(DEV_3357: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.06 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1935 6.31 %
Rwork0.189 --
obs0.192 30660 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 12 195 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112352
X-RAY DIFFRACTIONf_angle_d0.9983186
X-RAY DIFFRACTIONf_dihedral_angle_d18.182870
X-RAY DIFFRACTIONf_chiral_restr0.058352
X-RAY DIFFRACTIONf_plane_restr0.007410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.37241310.36621900X-RAY DIFFRACTION90
1.845-1.89490.31751320.32611848X-RAY DIFFRACTION91
1.8949-1.95070.30861330.28051975X-RAY DIFFRACTION93
1.9507-2.01360.3371300.25831955X-RAY DIFFRACTION94
2.0136-2.08560.23411380.22452018X-RAY DIFFRACTION96
2.0856-2.16910.24811320.20042007X-RAY DIFFRACTION96
2.1691-2.26780.22651350.18122039X-RAY DIFFRACTION97
2.2678-2.38740.22461410.17182079X-RAY DIFFRACTION97
2.3874-2.53690.2211410.16532068X-RAY DIFFRACTION98
2.5369-2.73280.21341360.1642085X-RAY DIFFRACTION98
2.7328-3.00770.18831410.1592129X-RAY DIFFRACTION99
3.0077-3.44280.21461430.15612131X-RAY DIFFRACTION99
3.4428-4.33690.17611470.15132183X-RAY DIFFRACTION100
4.3369-43.07580.23921550.18382308X-RAY DIFFRACTION100
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)
14.57390.557-0.40484.5993-1.77293.9021-0.0011-0.022-0.05680.06310.0042-0.30410.07960.3621-0.06040.02970.0067-0.0090.16960.01110.085816.619223.659629.4802
28.05885.4278-0.36685.52340.19740.56110.01550.0481-0.16380.0483-0.0469-0.22980.24390.19840.07230.09830.0284-0.02710.1630.02020.111722.395519.835923.6096
37.4078-0.5938-2.69873.30351.54315.7399-0.03880.52360.0461-0.26660.0708-0.3243-0.05770.1975-0.01020.10530.01520.01080.21250.03890.107218.539126.696618.376
41.6253-0.0359-1.06664.08990.43473.55620.0772-0.02320.1615-0.122-0.0881-0.2889-0.44110.2578-0.0060.1144-0.0361-0.01590.19610.03210.116114.389535.450520.3619
50.40790.538-0.41223.9219-4.50495.3060.08020.17530.33710.64950.58350.9762-0.8308-1.1083-0.65370.32670.13660.08160.35880.08670.31635.725441.608924.6985
62.65221.7846-2.33581.869-3.17496.8244-0.07310.10520.15580.08620.18150.1009-0.4132-0.5931-0.20350.09950.0580.01260.15350.01150.11974.642931.011726.3841
75.9927-0.16171.30025.59422.02672.6647-0.20890.32580.0148-0.39580.00340.16470.3787-0.69730.06640.0968-0.06720.01090.23640.00170.12773.808218.2528.4379
85.147-0.9675-0.04254.34930.89455.88110.03990.10820.05350.01-0.00750.1742-0.0232-0.3617-0.07860.0242-0.0086-0.00730.14190.00160.080114.047821.023245.8382
96.0209-6.1248-3.85399.37193.69999.244-0.0592-0.1352-0.053-0.09270.2119-0.08960.5422-0.1746-0.13180.0994-0.0378-0.01850.1299-0.01830.117614.896612.613347.8307
106.93082.0455-2.40671.0336-1.55483.3367-0.0398-0.2744-0.016-0.01490.02320.1950.0744-0.2914-0.06140.11510.01120.02280.2091-0.00460.11359.181119.728755.6283
117.7942-0.2683-3.12263.62410.86093.60140.2079-0.77980.76750.5633-0.10240.6624-1.2521-0.3047-0.0280.47090.06490.06480.219-0.08110.334914.046336.340858.5496
122.0555-0.778-0.00233.3351-0.84054.9951-0.0905-0.18230.23470.22650.0147-0.0142-0.4984-0.14940.04160.0791-0.0187-0.01090.218-0.02980.095119.888727.016156.5128
134.409-1.17291.29376.4831-0.94732.8545-0.2133-0.30730.63290.3710.2786-0.3954-0.98410.5095-0.04190.2983-0.0452-0.04010.2698-0.09490.217223.381733.293362.5201
141.5414-0.483-0.3261.4299-1.09913.4189-0.10290.04070.03340.1595-0.06570.0138-0.21130.201-0.0201-0.032-0.02950.01420.25570.02270.155527.783824.286742.833
157.8398-1.31412.17946.6868-1.38393.6368-0.13260.1004-0.32820.10450.0974-0.21960.54980.52650.15650.0760.03460.02810.2126-0.00370.165526.895515.525345.0593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 586 )
2X-RAY DIFFRACTION2chain 'A' and (resid 587 through 602 )
3X-RAY DIFFRACTION3chain 'A' and (resid 603 through 622 )
4X-RAY DIFFRACTION4chain 'A' and (resid 623 through 658 )
5X-RAY DIFFRACTION5chain 'A' and (resid 659 through 669 )
6X-RAY DIFFRACTION6chain 'A' and (resid 670 through 687 )
7X-RAY DIFFRACTION7chain 'A' and (resid 688 through 700 )
8X-RAY DIFFRACTION8chain 'B' and (resid 561 through 586 )
9X-RAY DIFFRACTION9chain 'B' and (resid 587 through 593 )
10X-RAY DIFFRACTION10chain 'B' and (resid 594 through 622 )
11X-RAY DIFFRACTION11chain 'B' and (resid 623 through 637 )
12X-RAY DIFFRACTION12chain 'B' and (resid 638 through 664 )
13X-RAY DIFFRACTION13chain 'B' and (resid 665 through 677 )
14X-RAY DIFFRACTION14chain 'B' and (resid 678 through 687 )
15X-RAY DIFFRACTION15chain 'B' and (resid 688 through 700 )

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