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- EMDB-39498: Structure of PsSIR2 tetradecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-39498
TitleStructure of PsSIR2 tetradecamer
Map data
Sample
  • Complex: PsSIR2 tetradecamer
    • Protein or peptide: SIR2-like domain-containing protein
Keywordscell growth inhibition / IMMUNE SYSTEM
Function / homologySIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein
Function and homology information
Biological speciesPaenibacillus sp. 453mf (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 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: Structure of a bacterial protein
Authors: Yu G / Liao F / Li X / Li Z / Zhang H
History
DepositionMar 19, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39498.png

Downloads & links

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Map

FileDownload / File: emd_39498.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 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: 0.13
Minimum - Maximum-0.5329845 - 1.4560341
Average (Standard dev.)-0.0013216258 (±0.03511218)
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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Sample components

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Entire : PsSIR2 tetradecamer

EntireName: PsSIR2 tetradecamer
Components
  • Complex: PsSIR2 tetradecamer
    • Protein or peptide: SIR2-like domain-containing protein

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Supramolecule #1: PsSIR2 tetradecamer

SupramoleculeName: PsSIR2 tetradecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)

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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: 14 / 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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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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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