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- EMDB-40763: E. coli SIR2-HerA complex (dodecamer SIR2 pentamer HerA) -

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Basic information

Entry
Database: EMDB / ID: EMD-40763
TitleE. coli SIR2-HerA complex (dodecamer SIR2 pentamer HerA)
Map data
Sample
  • Complex: SIR2-HerA complex 2(12:5)
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Nucleoside triphosphate hydrolase
  • Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHerA / SIR2 / NADase / ATPase / Anti-phage system / IMMUNE SYSTEM
Function / homologyHelicase HerA, central domain / Helicase HerA, central domain / SIR2-like domain / SIR2-like domain / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / SIR2-like domain-containing protein / Nucleoside triphosphate hydrolase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 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 11, 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_40763.png

Downloads & links

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Map

FileDownload / File: emd_40763.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.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.264
Minimum - Maximum-1.9782091 - 2.655368
Average (Standard dev.)0.0018924562 (±0.09025861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40763_additional_1.map
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Half map: #2

Fileemd_40763_half_map_1.map
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Half map: #1

Fileemd_40763_half_map_2.map
Projections & Slices
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Sample components

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Entire : SIR2-HerA complex 2(12:5)

EntireName: SIR2-HerA complex 2(12:5)
Components
  • Complex: SIR2-HerA complex 2(12:5)
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Nucleoside triphosphate hydrolase
  • Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SIR2-HerA complex 2(12:5)

SupramoleculeName: SIR2-HerA complex 2(12:5) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: pentamer HerA and dodecamer Sir2 form a complex
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: Nucleoside triphosphate hydrolase

MacromoleculeName: Nucleoside triphosphate hydrolase / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 68.431992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLFKLTEIS AIGYVVGLEG ERIRINLHEG LQGRLASHRK GVSSVTQPGD LIGFDAGNIL VVARVTDMAF VEADKAHKAN VGTSDLADI PLRQIIAYAI GFVKRELNGY VFISEDWRLP ALGSSAVPLT SDFLNIIYSI DKEELPKAVE LGVDSRTKTV K IFASVDKL ...String:
MSLFKLTEIS AIGYVVGLEG ERIRINLHEG LQGRLASHRK GVSSVTQPGD LIGFDAGNIL VVARVTDMAF VEADKAHKAN VGTSDLADI PLRQIIAYAI GFVKRELNGY VFISEDWRLP ALGSSAVPLT SDFLNIIYSI DKEELPKAVE LGVDSRTKTV K IFASVDKL LSRHLAVLGS TGYGKSNFNA LLTRKVSEKY PNSRIVIFDI NGEYAQAFTG IPNVKHTILG ESPNVDSLEK KQ QKGELYS EEYYCYKKIP YQALGFAGLI KLLRPSDKTQ LPALRNALSA INRTHFKSRN IYLEKDDGET FLLYDDCRDT NQS KLAEWL DLLRRRRLKR TNVWPPFKSL ATLVAEFGCV AADRSNGSKR DAFGFSNVLP LVKIIQQLAE DIRFKSIVNL NGGG ELADG GTHWDKAMSD EVDYFFGKEK GQENDWNVHI VNMKNLAQDH APMLLSALLE MFAEILFRRG QERSYPTVLL LEEAH HYLR DPYAEIDSQI KAYERLAKEG RKFKCSLIVS TQRPSELSPT VLAMCSNWFS LRLTNERDLQ ALRYAMESGN EQILKQ ISG LPRGDAVAFG SAFNLPVRIS INQARPGPKS SDAVFSEEWA NCTELRC

UniProtKB: Nucleoside triphosphate hydrolase

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Macromolecule #3: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]ME...

MacromoleculeName: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
type: ligand / ID: 3 / Number of copies: 12 / Formula: AR6
Molecular weightTheoretical: 559.316 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200494
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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