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- EMDB-17370: C. elegans TIR-1 protein. -

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Basic information

Entry
Database: EMDB / ID: EMD-17370
TitleC. elegans TIR-1 protein.
Map data
Sample
  • Complex: C. elegans TIR1.
    • Protein or peptide: NAD(+) hydrolase tir-1
KeywordsSARM1 / TIR-1 / C. elegans / neurodegeneration / cryo-EM / structural biology / NAD+ metabolism / axon Wallerian degeneration / HYDROLASE
Function / homology
Function and homology information


serotonin biosynthetic process / negative regulation of MyD88-independent toll-like receptor signaling pathway / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / cell fate specification / response to axon injury / defense response to fungus ...serotonin biosynthetic process / negative regulation of MyD88-independent toll-like receptor signaling pathway / NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / cell fate specification / response to axon injury / defense response to fungus / signaling adaptor activity / axon cytoplasm / protein localization / small GTPase binding / cell-cell signaling / cell body / nervous system development / defense response to Gram-negative bacterium / defense response to bacterium / axon / negative regulation of gene expression / innate immune response / dendrite / positive regulation of gene expression / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Sterile alpha and TIR motif-containing protein 1 / TIR domain / SAM domain (Sterile alpha motif) / 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 and TIR motif-containing protein 1 / TIR domain / SAM domain (Sterile alpha motif) / 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 tir-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsIsupov MN / Opatowsky Y
Funding support Israel, United States, 3 items
OrganizationGrant numberCountry
Israel Science Foundation1425/15 Israel
Israel Science Foundation909/19 Israel
United States - Israel Binational Science Foundation (BSF)2019150 United States
CitationJournal: Cell Rep / Year: 2023
Title: Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans.
Authors: Tami Khazma / Atira Grossman / Julia Guez-Haddad / Chengye Feng / Hadas Dabas / Radhika Sain / Michal Weitman / Ran Zalk / Michail N Isupov / Marc Hammarlund / Michael Hons / Yarden Opatowsky /
Abstract: Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed ...Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed in C. elegans (ceSARM/ceTIR-1). We hypothesized that differences in SARM between species might exist and account for the divergence in WD. We first show that expression of the human (h)SARM1, but not ceTIR-1, in C. elegans neurons is sufficient to confer axon degeneration after nerve injury. Next, we determined the cryoelectron microscopy structure of ceTIR-1 and found that, unlike hSARM1, which exists as an auto-inhibited ring octamer, ceTIR-1 forms a readily active 9-mer. Enzymatically, the NADase activity of ceTIR-1 is substantially weaker (10-fold higher Km) than that of hSARM1, and even when fully active, it falls short of consuming all cellular NAD. Our experiments provide insight into the molecular mechanisms and evolution of SARM orthologs and WD across species.
History
DepositionMay 16, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17370.png

Downloads & links

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Map

FileDownload / File: emd_17370.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.20065366 - 0.5108465
Average (Standard dev.)0.0026274212 (±0.028278505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17370_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17370_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : C. elegans TIR1.

EntireName: C. elegans TIR1.
Components
  • Complex: C. elegans TIR1.
    • Protein or peptide: NAD(+) hydrolase tir-1

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Supramolecule #1: C. elegans TIR1.

SupramoleculeName: C. elegans TIR1. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: NAD(+) hydrolase tir-1

MacromoleculeName: NAD(+) hydrolase tir-1 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO / EC number: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 84.496172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSYHHHHHHD YDIPTTENLY FQGAMGSHMD ELSPVDQRST SGTARFLIQQ DSVVNPSTKM SNTEQVAMMH TLKTKLSKYQ AMMDKAFEE IAKVEDANII EGCTIVRKLM RKVWNTPKVS ADLANALCDY LRDRDYFDKL IKMFISPNTA ACDQVRMECG K VLEECTSS ...String:
MSYHHHHHHD YDIPTTENLY FQGAMGSHMD ELSPVDQRST SGTARFLIQQ DSVVNPSTKM SNTEQVAMMH TLKTKLSKYQ AMMDKAFEE IAKVEDANII EGCTIVRKLM RKVWNTPKVS ADLANALCDY LRDRDYFDKL IKMFISPNTA ACDQVRMECG K VLEECTSS ANLEYIVNKS YTKKIMIVAM KLNKTPDQQR LSLSLIGNLF KHSNAVSLSL IETDVIDHII LTFKRAPECP DI LRHAALA LANILLYTCF EGKKKIIQKK IPEWLFFLAS QADDVTRYYA CIAVCTIVSV KEFEPLVRKS DTMKLVEPFL QVH DPATFA RDYHKYAQGN TKEWLERLLP MLQPSRRREA RSVAAFHFTL EATIKKEQNK LDVFQEIGAI QALKEVASSP DEVA AKFAS EALTVIGEEV PYKLAQQVPG WTCADVQYWV KKIGFEEYVE KFAKQMVDGD LLLQLTENDL KHDVGMISGL HRKRF LREL QTLKVAADYS SVDESNLDNF LMGLSPELSV YTYQMLTNGV NRSLLSSLTD EMMQNACGIT NPIHRLKLTQ AFETAK HPD DVEVAMLSKQ IDVFISYRRS TGNQLASLIK VLLQLRGYRV FIDVDKLYAG KFDSSLLKNI QAAKHFILVL TPNSLDR LL NDDNCEDWVH KELKCAFEHQ KNIIPIFDTA FEFPTKEDQI PNDIRMITKY NGVKWVHDYQ DACMAKVVRF ITGELNRT T PTTKEMPSIS RKTTQQR

UniProtKB: NAD(+) hydrolase tir-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 370021
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121487
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8p2m:
C. elegans TIR-1 protein.

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