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

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Basic information

Entry
Database: PDB / ID: 7rtc
TitleCrystal structure of the ARM domain from Drosophila SARM1 in complex with NaMN
ComponentsNAD(+) hydrolase sarm1
KeywordsHYDROLASE / Axon degeneration / ARM domain / Inhibitor
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
NICOTINATE MONONUCLEOTIDE / NAD(+) hydrolase sarm1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsGu, W. / Ve, T. / 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)1196590 Australia
Australian Research Council (ARC)FL180100109 Australia
Australian Research Council (ARC)FT200100572 Australia
CitationJournal: Exp Neurol / Year: 2021
Title: Nicotinic acid mononucleotide is an allosteric SARM1 inhibitor promoting axonal protection.
Authors: Sasaki, Y. / Zhu, J. / Shi, Y. / Gu, W. / Kobe, B. / Ve, T. / DiAntonio, A. / Milbrandt, J.
History
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: 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: NAD(+) hydrolase sarm1
B: NAD(+) hydrolase sarm1
C: NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4196
Polymers120,4133
Non-polymers1,0063
Water00
1
A: NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4732
Polymers40,1381
Non-polymers3351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4732
Polymers40,1381
Non-polymers3351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NAD(+) hydrolase sarm1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4732
Polymers40,1381
Non-polymers3351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.122, 102.823, 100.198
Angle α, β, γ (deg.)90.000, 103.836, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLYA1 - 331
d_12ens_1NCNNCNB
d_21ens_1ALAGLYC1 - 331
d_22ens_1NCNNCND
d_31ens_1ALAGLYE1 - 331
d_32ens_1NCNNCNF

NCS oper:
IDCodeMatrixVector
1given(-0.387412527255, -0.862041568853, -0.32679636977), (0.851396755409, -0.470511911531, 0.231823437096), (-0.353603024033, -0.188422065259, 0.916221603499)27.5859863353, -25.7906964873, -27.1244976051
2given(0.411530007102, -0.8383076089, 0.357607894371), (-0.83671366294, -0.503065961413, -0.21641368884), (0.361321601215, -0.21015468429, -0.908450168785)43.813974056, 56.3774068044, -40.5191183939

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Components

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


Mass: 40137.645 Da / Num. of mol.: 3
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-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H14NO9P / Feature type: SUBJECT OF INVESTIGATION
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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.7 M sodium malonate pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.31→39.41 Å / Num. obs: 18295 / % possible obs: 92 % / Redundancy: 6.7 % / Biso Wilson estimate: 78.97 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.6
Reflection shellResolution: 3.31→3.58 Å / Num. unique obs: 3462 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LCY

7lcy


Resolution: 3.31→39.41 Å / SU ML: 0.4068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 934 5.12 %
Rwork0.2384 17312 -
obs0.2394 18246 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7683 0 66 0 7749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357878
X-RAY DIFFRACTIONf_angle_d0.600210653
X-RAY DIFFRACTIONf_chiral_restr0.03551221
X-RAY DIFFRACTIONf_plane_restr0.00361377
X-RAY DIFFRACTIONf_dihedral_angle_d12.56922874
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.744473853768
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.826692864815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.480.32111132069X-RAY DIFFRACTION77.9
3.48-3.70.28561112207X-RAY DIFFRACTION81.91
3.7-3.990.3164940.26872297X-RAY DIFFRACTION84.64
3.99-4.390.26841540.2292657X-RAY DIFFRACTION99.96
4.39-5.020.25331440.21852677X-RAY DIFFRACTION99.75
5.02-6.320.28471440.26012703X-RAY DIFFRACTION99.93
6.33-39.410.21361740.1992702X-RAY DIFFRACTION99.38

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