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- EMDB-39290: Cryo-EM structure of the trimeric HerA -

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Basic information

Entry
Database: EMDB / ID: EMD-39290
TitleCryo-EM structure of the trimeric HerA
Map data
Sample
  • Complex: Cryo-Em structure of the trimeric HerA
    • Protein or peptide: DUF87 domain-containing protein
Keywordsantiphage system / IMMUNE SYSTEM
Function / homology:
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhen X / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)321700145 China
CitationJournal: Nat Commun / Year: 2024
Title: Mechanistic basis for the allosteric activation of NADase activity in the Sir2-HerA antiphage defense system.
Authors: Xiangkai Zhen / Biao Zhou / Zihe Liu / Xurong Wang / Heyu Zhao / Shuxian Wu / Zekai Li / Jiamin Liang / Wanyue Zhang / Qingjian Zhu / Jun He / Xiaoli Xiong / Songying Ouyang /
Abstract: Sir2-HerA is a widely distributed antiphage system composed of a RecA-like ATPase (HerA) and an effector with potential NADase activity (Sir2). Sir2-HerA is believed to provide defense against phage ...Sir2-HerA is a widely distributed antiphage system composed of a RecA-like ATPase (HerA) and an effector with potential NADase activity (Sir2). Sir2-HerA is believed to provide defense against phage infection in Sir2-dependent NAD depletion to arrest the growth of infected cells. However, the detailed mechanism underlying its antiphage activity remains largely unknown. Here, we report functional investigations of Sir2-HerA from Staphylococcus aureus (SaSir2-HerA), unveiling that the NADase function of SaSir2 can be allosterically activated by the binding of SaHerA, which then assembles into a supramolecular complex with NADase activity. By combining the cryo-EM structure of SaSir2-HerA in complex with the NAD cleavage product, it is surprisingly observed that Sir2 protomers that interact with HerA are in the activated state, which is due to the opening of the α15-helix covering the active site, allowing NAD to access the catalytic pocket for hydrolysis. In brief, our study provides a comprehensive view of an allosteric activation mechanism for Sir2 NADase activity in the Sir2-HerA immune system.
History
DepositionFeb 28, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39290.png

Downloads & links

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Map

FileDownload / File: emd_39290.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 360 pix.
= 255.6 Å		0.71 Å/pix.
x 360 pix.
= 255.6 Å		0.71 Å/pix.
x 360 pix.
= 255.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0163
Minimum - Maximum-0.21574448 - 0.41628298
Average (Standard dev.)-0.00014750905 (±0.008175356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 255.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39290_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39290_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_39290_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-Em structure of the trimeric HerA

EntireName: Cryo-Em structure of the trimeric HerA
Components
  • Complex: Cryo-Em structure of the trimeric HerA
    • Protein or peptide: DUF87 domain-containing protein

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Supramolecule #1: Cryo-Em structure of the trimeric HerA

SupramoleculeName: Cryo-Em structure of the trimeric HerA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: DUF87 domain-containing protein

MacromoleculeName: DUF87 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 65.255168 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHSIGKVTSV TFEKLIFEVS DFEKLNYNLL GQIYIAKGVI DYVTIKNEYS EKFIYQVVKV EDKEIPLSSE EHSKFKYHGR FECVPVGMI KHGKIEFNLK KYPFLQDKVY LTSQEEMEMV FSHFHNGNDI TIGLIDDQYP AYFNTAKLLT NHTAIIGNTG S GKSTTVRQ ...String:
MHSIGKVTSV TFEKLIFEVS DFEKLNYNLL GQIYIAKGVI DYVTIKNEYS EKFIYQVVKV EDKEIPLSSE EHSKFKYHGR FECVPVGMI KHGKIEFNLK KYPFLQDKVY LTSQEEMEMV FSHFHNGNDI TIGLIDDQYP AYFNTAKLLT NHTAIIGNTG S GKSTTVRQ IISKINNLNT QNLHFHIFDV HDEYKDINGV KIVDVINDFK INIKNLEMQD WINLIKPSEL VQLPILQMGL KY ANAIENK IIEEEWLKCY IALSLYRNQQ TDAVTKRTKI LSILDGTNID TEKYDSKYGN MDSNTEKKFI ESLKNVVDNG GNI FTLSEV IEKAKYNVSS FNKLLEGLNY VFLLEESKGN NQARSYSATL ETRIKNVQTR FSNLFGNNDT ELEDKSIVYS VSEL DDDLL LFFTTFILKK EFEKNKKMKL EDRSVNVFIF EEAHRYISKF KESSQFNEVE AFKKIAREGR KFGCFLMLSS QRPSE LSST VLSQCNNYIV HRVKNNVDLE YLLNSIPYIN KFQLNRFSYL PTGTAYIVGE LFPIPVEIEI FEEFSKNSTI TPEIVY RS

UniProtKB: UNIPROTKB: A0A844QRL0

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.4 µm / Nominal defocus min: 0.8 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 486514
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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