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- EMDB-37616: Cryo-EM structure of SIR2/HerA antiphage complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37616
TitleCryo-EM structure of SIR2/HerA antiphage complex
Map datamain map
Sample
  • Complex: Cryo-EM structure of SIR2/HerA complex
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Helicase HerA central domain-containing protein
Keywordsbacterial immune proteins / IMMUNE SYSTEM
Function / homology
Function and homology information


helicase activity / hydrolase activity / ATP binding
Similarity search - Function
Helicase HerA-like C-terminal / Helicase HerA-like C-terminal / KTSC domain / KTSC domain / Helicase HerA-like / Helicase HerA, central domain / Helicase HerA, central domain / SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SIR2-like domain-containing protein / Helicase HerA central domain-containing protein
Similarity search - Component
Biological speciesPaenibacillus sp. 453mf (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsYu G / Liao F / Li X / Li Z / Zhang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200496 China
CitationJournal: To Be Published
Title: Cryo-EM structure of SIR2/HerA antiphage complex
Authors: Yu G / Liao F / Li X / Li Z / Zhang H
History
DepositionSep 29, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37616.png

Downloads & links

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Map

FileDownload / File: emd_37616.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 440 pix.
= 435.2 Å		0.99 Å/pix.
x 440 pix.
= 435.2 Å		0.99 Å/pix.
x 440 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98909 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0856199 - 2.19133
Average (Standard dev.)-0.00075733755 (±0.062766336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 435.19962 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_37616_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_37616_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SIR2/HerA complex

EntireName: Cryo-EM structure of SIR2/HerA complex
Components
  • Complex: Cryo-EM structure of SIR2/HerA complex
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Helicase HerA central domain-containing protein

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Supramolecule #1: Cryo-EM structure of SIR2/HerA complex

SupramoleculeName: Cryo-EM structure of SIR2/HerA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 400 KDa

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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: 9 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 43.60948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDHSITASYY DTTQQLSLLK HVLSEDKRPI AFIIAAGCPV SIRHNDAPLI PDVAGLTRKI SDSFGGNPDS LLMKIIQNLK TTIPNPTIE DILSYIRLLQ QIPMSGKIHD VENSVINALE ESICELIEEE VNVDLPGNAT PYHKIAAWIN SINREHQVEI F TTNYDLLM ...String:
MDHSITASYY DTTQQLSLLK HVLSEDKRPI AFIIAAGCPV SIRHNDAPLI PDVAGLTRKI SDSFGGNPDS LLMKIIQNLK TTIPNPTIE DILSYIRLLQ QIPMSGKIHD VENSVINALE ESICELIEEE VNVDLPGNAT PYHKIAAWIN SINREHQVEI F TTNYDLLM EQALEELNVP YFDGFVGSKR AFFDIRTIEE NKLPSRWSKL WKLHGSINWQ LDKQTQTIWR GTPSKGCSLI HP SHLKYDQ SRKMPYLVMM DQLKLFLNQP SAILITCGYS YKDQHINEVL SQGLQTNPNA LIYGLQYDVL ENYQEAKDMA LKR SNLILL AKDRAIIGKK EGEWKPDPQS SQDNDPLLFF KLGDFQHLAS FLEEISQYDW SKQND

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: Helicase HerA central domain-containing protein

MacromoleculeName: Helicase HerA central domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 77.626344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS ...String:
MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS TGSGKSTTVT SILQRISDMS QFPSARIIVF DIHGEYAAAF KGKAKVYKVT PSNNELKLSI PYWALTCDEF LS VAFGGLE GSGRNALIDK IYELKLQTLK RQEYEGINED SLTVDTPIPF SIHKLWFDLY RAEISTHYVQ GSHSEENEAL LLG EDGNPV QKGDSLKVVP PIYMPHTQAQ GATKIYLSNR GKNIRKPLEG LASLLKDPRY EFLFNADDWS VNLDGKTNKD LDAL LETWV GSEESISIFD LSGMPSSILD TLIGILIRIL YDSLFWSRNQ PEGGRERPLL VVLEEAHTYL GKDSRGIAID GVRKI VKEG RKYGIGMMLV SQRPSEIDST ILSQCGTLFA LRMNNSSDRN HVLGAVSDSF EGLMGMLPTL RTGEAIIIGE SVRLPM RTI ISPPPFGRRP DSLDPDVTAK WSNNRVQGDY KEVLTLWRQK KVRSQRIVEN IKRLPVVNEG EMTDMVREMV TSSNILS IG YEADSMTLEI EFNHGLVYQY YDVPETLHTE LLAAESHGKF FNSQIKNNYR FSRI

UniProtKB: Helicase HerA central domain-containing protein

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35127
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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