+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21863 | ||||||||||||
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Title | SARM1 Autoinhibited Conformation | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | NADase / ARM / SAM / TIR / HYDROLASE | ||||||||||||
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 / 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 / mitochondrial outer membrane / microtubule / cell differentiation / axon / innate immune response / dendrite / synapse / cell surface / signal transduction / protein-containing complex / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Xie T / Bratkowski M | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural and Mechanistic Regulation of the Pro-degenerative NAD Hydrolase SARM1. Authors: Matthew Bratkowski / Tian Xie / Desiree A Thayer / Shradha Lad / Prakhyat Mathur / Yu-San Yang / Gregory Danko / Thomas C Burdett / Jean Danao / Aaron Cantor / Jennifer A Kozak / Sean P ...Authors: Matthew Bratkowski / Tian Xie / Desiree A Thayer / Shradha Lad / Prakhyat Mathur / Yu-San Yang / Gregory Danko / Thomas C Burdett / Jean Danao / Aaron Cantor / Jennifer A Kozak / Sean P Brown / Xiaochen Bai / Shilpa Sambashivan / Abstract: The NADase SARM1 is a central switch in injury-activated axon degeneration, an early hallmark of many neurological diseases. Here, we present cryo-electron microscopy (cryo-EM) structures of ...The NADase SARM1 is a central switch in injury-activated axon degeneration, an early hallmark of many neurological diseases. Here, we present cryo-electron microscopy (cryo-EM) structures of autoinhibited (3.3 Å) and active SARM1 (6.8 Å) and provide mechanistic insight into the tight regulation of SARM1's function by the local metabolic environment. Although both states retain an octameric core, the defining feature of the autoinhibited state is a lock between the autoinhibitory Armadillo/HEAT motif (ARM) and catalytic Toll/interleukin-1 receptor (TIR) domains, which traps SARM1 in an inactive state. Mutations that break this lock activate SARM1, resulting in catastrophic neuronal death. Notably, the mutants cannot be further activated by the endogenous activator nicotinamide mononucleotide (NMN), and active SARM1 is product inhibited by Nicotinamide (NAM), highlighting SARM1's functional dependence on key metabolites in the NAD salvage pathway. Our studies provide a molecular understanding of SARM1's transition from an autoinhibited to an injury-activated state and lay the foundation for future SARM1-based therapies to treat axonopathies. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21863.map.gz | 62.7 MB | EMDB map data format | |
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Header (meta data) | emd-21863-v30.xml emd-21863.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21863_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_21863.png | 146.1 KB | ||
Filedesc metadata | emd-21863.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21863 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21863 | HTTPS FTP |
-Validation report
Summary document | emd_21863_validation.pdf.gz | 608.1 KB | Display | EMDB validaton report |
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Full document | emd_21863_full_validation.pdf.gz | 607.7 KB | Display | |
Data in XML | emd_21863_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_21863_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21863 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21863 | HTTPS FTP |
-Related structure data
Related structure data | 6wpkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21863.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARM1 in an autoinhibited conformation
Entire | Name: SARM1 in an autoinhibited conformation |
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Components |
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-Supramolecule #1: SARM1 in an autoinhibited conformation
Supramolecule | Name: SARM1 in an autoinhibited conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: NAD(+) hydrolase SARM1
Macromolecule | Name: NAD(+) hydrolase SARM1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 75.679594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGPREVSPGA GTEVQDALER ALPELQQALS ALKQAGGARA VGAGLAEVFQ LVEEAWLLPA VGREVAQGLC DAIRLDGGLD LLLRLLQAP ELETRVQAAR LLEQILVAEN RDRVARIGLG VILNLAKERE PVELARSVAG ILEHMFKHSE ETCQRLVAAG G LDAVLYWC ...String: MGPREVSPGA GTEVQDALER ALPELQQALS ALKQAGGARA VGAGLAEVFQ LVEEAWLLPA VGREVAQGLC DAIRLDGGLD LLLRLLQAP ELETRVQAAR LLEQILVAEN RDRVARIGLG VILNLAKERE PVELARSVAG ILEHMFKHSE ETCQRLVAAG G LDAVLYWC RRTDPALLRH CALALGNCAL HGGQAVQRRM VEKRAAEWLF PLAFSKEDEL LRLHACLAVA VLATNKEVER EV ERSGTLA LVEPLVASLD PGRFARCLVD ASDTSQGRGP DDLQRLVPLL DSNRLEAQCI GAFYLCAEAA IKSLQGKTKV FSD IGAIQS LKRLVSYSTN GTKSALAKRA LRLLGEEVPR PILPSVPSWK EAEVQTWLQQ IGFSKYCESF REQQVDGDLL LRLT EEELQ TDLGMKSGIT RKRFFRELTE LKTFANYSTC DRSNLADWLG SLDPRFRQYT YGLVSCGLDR SLLHRVSEQQ LLEDC GIHL GVHRARILTA AREMLHSPLP CTGGKPSGDT PDVFISYRRN SGSQLASLLK VHLQLHGFSV FIDVEKLEAG KFEDKL IQS VMGARNFVLV LSPGALDKCM QDHDCKDWVH KEIVTALSCG KNIVPIIDGF EWPEPQVLPE DMQAVLTFNG IKWSHEY QE ATIEKIIRFL QGRSSRDSSA GSDTSLEGAA PMGPTGGSEN LYFQ UniProtKB: NAD(+) hydrolase SARM1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 46729 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |