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- PDB-7uxu: CryoEM structure of the TIR domain from AbTir in complex with 3AD -

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Basic information

Entry
Database: PDB / ID: 7uxu
TitleCryoEM structure of the TIR domain from AbTir in complex with 3AD
ComponentsMolecular chaperone Tir
KeywordsHYDROLASE / 2' cADPR / NADase / Bacterial TIR
Function / homology
Function and homology information


NAD+ catabolic process / NAD+ nucleosidase activity / signal transduction
Similarity search - Function
TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
Chem-1O4 / Molecular chaperone Tir
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsLi, S. / Nanson, J.D. / Manik, M.K. / Gu, W. / Landsberg, M.J. / Ve, T. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
CitationJournal: Science / Year: 2022
Title: Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.
Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / ...Authors: Mohammad K Manik / Yun Shi / Sulin Li / Mark A Zaydman / Neha Damaraju / Samuel Eastman / Thomas G Smith / Weixi Gu / Veronika Masic / Tamim Mosaiab / James S Weagley / Steven J Hancock / Eduardo Vasquez / Lauren Hartley-Tassell / Nestoras Kargios / Natsumi Maruta / Bryan Y J Lim / Hayden Burdett / Michael J Landsberg / Mark A Schembri / Ivan Prokes / Lijiang Song / Murray Grant / Aaron DiAntonio / Jeffrey D Nanson / Ming Guo / Jeffrey Milbrandt / Thomas Ve / Bostjan Kobe /
Abstract: Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide ...Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molecular chaperone Tir
B: Molecular chaperone Tir
C: Molecular chaperone Tir
D: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2048
Polymers62,4584
Non-polymers2,7464
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 4 / Rise per n subunits: 17.8 Å / Rotation per n subunits: 174 °)

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Components

#1: Protein
Molecular chaperone Tir / TIR domain-containing protein


Mass: 15614.538 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: APD31_10100, H0529_09530 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q1J3X1
#2: Chemical
ChemComp-1O4 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(8-azanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 686.482 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament of the AbTIR TIR domain in complex with 3AD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 96 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 4000 nm / Nominal defocus min: 100 nm / Cs: 2.7 mm
Image recordingElectron dose: 40.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
7ISOLDEmodel fitting
12cryoSPARCv3.3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 174.056 ° / Axial rise/subunit: 17.867 Å / Axial symmetry: C1
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272949 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514612
ELECTRON MICROSCOPYf_angle_d0.89136292
ELECTRON MICROSCOPYf_chiral_restr0.0505716
ELECTRON MICROSCOPYf_plane_restr0.0078884
ELECTRON MICROSCOPYf_dihedral_angle_d12.74861776

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