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- EMDB-40860: E. coli dodecamer SIR2 -

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Basic information

Entry
Database: EMDB / ID: EMD-40860
TitleE. coli dodecamer SIR2
Map data
Sample
  • Complex: E. coli dodecamer SIR2
    • Protein or peptide: SIR2-like domain-containing protein
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsSIR2 / NADase / Nuclease / Anti-phage system / IMMUNE SYSTEM
Function / homologySIR2-like domain / SIR2-like domain / SIR2-like domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShen ZF / Lin QP / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2023
Title: Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense.
Authors: Zhangfei Shen / Qingpeng Lin / Xiao-Yuan Yang / Elizabeth Fosuah / Tian-Min Fu /
Abstract: SIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex ...SIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex reveals a dynamic assembly process. Unlike other ATPases, HerA can form various oligomers, ranging from dimers to nonamers. When assembled with SIR2, HerA forms a hexamer and converts SIR2 from a nuclease to an NAD hydrolase, representing an unexpected regulatory mechanism mediated by protein assembly. Furthermore, high concentrations of ATP can inhibit NAD hydrolysis by the SIR2-HerA complex. Cryo-EM structures of the SIR2-HerA complex reveal a giant supramolecular assembly up to 1 MDa, with SIR2 as a dodecamer and HerA as a hexamer, crucial for anti-phage defense. Unexpectedly, the HerA hexamer resembles a spiral staircase and exhibits helicase activities toward dual-forked DNA. Together, we reveal the supramolecular assembly of SIR2-HerA as a unique mechanism for switching enzymatic activities and bolstering anti-phage defense strategies.
History
DepositionMay 24, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40860.png

Downloads & links

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Map

FileDownload / File: emd_40860.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.4495 Å
Density
Contour LevelBy AUTHOR: 0.0188
Minimum - Maximum-0.09214316 - 0.12349946
Average (Standard dev.)0.0003361015 (±0.0036728333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 323.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40860_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_40860_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40860_half_map_2.map
Projections & Slices
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Sample components

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Entire : E. coli dodecamer SIR2

EntireName: E. coli dodecamer SIR2
Components
  • Complex: E. coli dodecamer SIR2
    • Protein or peptide: SIR2-like domain-containing protein
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: E. coli dodecamer SIR2

SupramoleculeName: E. coli dodecamer SIR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Six dimeric SIR2 form a dodecamer
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.817664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIYQGGNKL NEDDFRSHVY SLCQLDNVGV LLGAGASVGC GGKTMKDVWK SFKQNYPELL GALIDKYLLV SQIDSDNNLV NVELLIDEA TKFLSVAKTR RCEDEEEEFR KILSSLYKEV TKAALLTGEQ FREKNQGKKD AFKYHKELIS KLISNRQPGQ S APAIFTTN ...String:
MSIYQGGNKL NEDDFRSHVY SLCQLDNVGV LLGAGASVGC GGKTMKDVWK SFKQNYPELL GALIDKYLLV SQIDSDNNLV NVELLIDEA TKFLSVAKTR RCEDEEEEFR KILSSLYKEV TKAALLTGEQ FREKNQGKKD AFKYHKELIS KLISNRQPGQ S APAIFTTN YDLALEWAAE DLGIQLFNGF SGLHTRQFYP QNFDLAFRNV NAKGEARFGH YHAYLYKLHG SLTWYQNDSL TV NEVSASQ AYDEYINDII NKDDFYRGQH LIYPGANKYS HTIGFVYGEM FRRFGEFISK PQTALFINGF GFGDYHINRI ILG ALLNPS FHVVIYYPEL KEAITKVSKG GGSEAEKAIV TLKNMAFNQV TVVGGGSKAY FNSFVEHLPY PVLFPRDNIV DELV EAIAN LSKGEGNVPF

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272075
FSC plot (resolution estimation)

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