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- PDB-7m6k: Crystal structure of the ARM domain from Drosophila SARM1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7m6k
TitleCrystal structure of the ARM domain from Drosophila SARM1 in complex with VMN
ComponentsIsoform B of NAD(+) hydrolase sarm1
KeywordsIMMUNE SYSTEM / neurotoxicity / axon degeneration / NADase / ARM domain
Function / homology
Function and homology information


negative regulation of MyD88-independent toll-like receptor signaling pathway / positive regulation of receptor signaling pathway via STAT / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / STAT family protein binding / antiviral innate immune response / response to axon injury / signaling adaptor activity ...negative regulation of MyD88-independent toll-like receptor signaling pathway / positive regulation of receptor signaling pathway via STAT / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / STAT family protein binding / antiviral innate immune response / response to axon injury / signaling adaptor activity / defense response to virus / neuron projection / axon / neuronal cell body / dendrite / signal transduction / cytosol
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-YRJ / NAD(+) hydrolase sarm1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGu, W. / Luo, Z. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1160570 Australia
Australian Research Council (ARC)FL180100109 Australia
CitationJournal: Elife / Year: 2021
Title: Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1.
Authors: Loreto, A. / Angeletti, C. / Gu, W. / Osborne, A. / Nieuwenhuis, B. / Gilley, J. / Merlini, E. / Arthur-Farraj, P. / Amici, A. / Luo, Z. / Hartley-Tassell, L. / Ve, T. / Desrochers, L.M. / ...Authors: Loreto, A. / Angeletti, C. / Gu, W. / Osborne, A. / Nieuwenhuis, B. / Gilley, J. / Merlini, E. / Arthur-Farraj, P. / Amici, A. / Luo, Z. / Hartley-Tassell, L. / Ve, T. / Desrochers, L.M. / Wang, Q. / Kobe, B. / Orsomando, G. / Coleman, M.P.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Isoform B of NAD(+) hydrolase sarm1
B: Isoform B of NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8186
Polymers68,8012
Non-polymers1,0174
Water3,495194
1
A: Isoform B of NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9324
Polymers34,4001
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform B of NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8862
Polymers34,4001
Non-polymers4851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.065, 51.010, 76.560
Angle α, β, γ (deg.)103.492, 101.784, 96.071
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 373 through 377 or resid 379...
d_2ens_1(chain "B" and (resid 373 through 377 or resid 379...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRILEA1 - 5
d_12ens_1GLUARGA7 - 10
d_13ens_1ALATYRA13 - 25
d_14ens_1LEULEUA27 - 40
d_15ens_1LYSPHEA42 - 51
d_16ens_1SERHISA53 - 92
d_17ens_1ARGPHEA95 - 105
d_18ens_1HISALAA107 - 140
d_19ens_1ALAHISA144 - 175
d_110ens_1ASPGLYA177 - 205
d_111ens_1LEUALAA208 - 229
d_112ens_1ALALYSA232 - 241
d_113ens_1LEUILEA243 - 309
d_114ens_1LIGLIGB
d_21ens_1TYRILEC4 - 8
d_22ens_1GLUARGC11 - 14
d_23ens_1ALATYRC16 - 28
d_24ens_1LEULEUC31 - 44
d_25ens_1LYSPHEC47 - 56
d_26ens_1SERHISC59 - 98
d_27ens_1ARGPHEC101 - 111
d_28ens_1HISALAC114 - 147
d_29ens_1ALAHISC151 - 182
d_210ens_1ASPGLYC185 - 213
d_211ens_1LEUALAC216 - 237
d_212ens_1ALALYSC239 - 248
d_213ens_1LEUILEC251 - 317
d_214ens_1LIGLIGD

NCS oper: (Code: givenMatrix: (0.163612446587, -0.773354923171, -0.612497453162), (-0.791312875985, -0.473634559675, 0.38664484502), (-0.589113655946, 0.421417212141, -0.689458217508)Vector: 18. ...NCS oper: (Code: given
Matrix: (0.163612446587, -0.773354923171, -0.612497453162), (-0.791312875985, -0.473634559675, 0.38664484502), (-0.589113655946, 0.421417212141, -0.689458217508)
Vector: 18.5266102319, 1.26413062241, -43.9722745442)

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Components

#1: Protein Isoform B of NAD(+) hydrolase sarm1 / NADase sarm1 / Sterile alpha and TIR motif-containing protein 1 / Tir-1 homolog


Mass: 34400.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sarm, Ect4, CG43119 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6IDD9, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Chemical ChemComp-YRJ / 3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium


Mass: 485.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N4O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 3350 and 0.2 M magnesium acetate tetrahydrate, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.69→46.6 Å / Num. obs: 60345 / % possible obs: 96.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rsym value: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.96 / Num. unique obs: 2695 / CC1/2: 0.69 / Rpim(I) all: 0.59 / Rsym value: 1.13

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LCZ

7lcz


Resolution: 1.69→36.36 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.6501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 3048 5.05 %
Rwork0.1895 57282 -
obs0.1912 60330 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 1.69→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 68 194 4994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00485009
X-RAY DIFFRACTIONf_angle_d0.85036798
X-RAY DIFFRACTIONf_chiral_restr0.0404766
X-RAY DIFFRACTIONf_plane_restr0.0051887
X-RAY DIFFRACTIONf_dihedral_angle_d16.15371846
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.695426880996 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.710.37591040.34932235X-RAY DIFFRACTION83.18
1.71-1.740.33321520.32542580X-RAY DIFFRACTION96.03
1.74-1.770.30381630.30722617X-RAY DIFFRACTION96.09
1.77-1.80.29681470.30042525X-RAY DIFFRACTION96.05
1.8-1.840.30251360.28582622X-RAY DIFFRACTION96.16
1.84-1.880.34011410.28062587X-RAY DIFFRACTION96.46
1.88-1.920.31581380.26352595X-RAY DIFFRACTION96.37
1.92-1.960.3081400.25712614X-RAY DIFFRACTION96.19
1.96-2.010.2651400.24972573X-RAY DIFFRACTION97.03
2.01-2.070.25361820.22732603X-RAY DIFFRACTION97.11
2.07-2.130.28511420.22062605X-RAY DIFFRACTION97.34
2.13-2.190.27771450.21942630X-RAY DIFFRACTION97.3
2.19-2.270.2621410.21172622X-RAY DIFFRACTION97.7
2.27-2.360.25351260.20742624X-RAY DIFFRACTION97.73
2.36-2.470.24481500.19992647X-RAY DIFFRACTION97.93
2.47-2.60.24581310.20012674X-RAY DIFFRACTION98.15
2.6-2.760.2181200.19692648X-RAY DIFFRACTION97.95
2.76-2.980.2291340.20142657X-RAY DIFFRACTION98.07
2.98-3.280.24331110.19372692X-RAY DIFFRACTION98.35
3.28-3.750.21681290.1732656X-RAY DIFFRACTION98.38
3.75-4.720.17141190.13922666X-RAY DIFFRACTION98.27
4.73-36.360.17661570.1532610X-RAY DIFFRACTION97.22

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