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- EMDB-67586: Cryo-EM reconstruction of the cyanophage Pam5 small terminase -

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Basic information

Entry
Database: EMDB / ID: EMD-67586
TitleCryo-EM reconstruction of the cyanophage Pam5 small terminase
Map dataCryo-EM reconstruction of the cyanophage Pam5 small terminase
Sample
  • Virus: Pseudanabaena phage Pam5 (virus)
    • Protein or peptide: Pam5 small terminase
KeywordsCyanophage / Virus / VIRAL PROTEIN / Terminase
Biological speciesPseudanabaena phage Pam5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDong DQ / Jiang YL / Zhou CZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
National Natural Science Foundation of China (NSFC)92451302 China
CitationJournal: Acta Biochim Biophys Sin (Shanghai) / Year: 2026
Title: Structural and functional insights into the distinct DNA recognition mechanisms of the terminase small subunit TerS from cyanophages.
Abstract: Efficient genome packaging is a critical step in the phage life cycle, directly influencing the viral maturation and infectivity. In tailed phages, this process is driven by a packaging motor ...Efficient genome packaging is a critical step in the phage life cycle, directly influencing the viral maturation and infectivity. In tailed phages, this process is driven by a packaging motor composed of a portal protein and a terminase complex. The terminase complex usually consists of a large subunit (TerL) and a small subunit (TerS), which cooperate to recognize, cleave, and translocate genomic DNA into the capsid. However, due to the remarkable diversity and complexity of phage packaging systems, the molecular mechanisms governing TerS-mediated DNA recognition remain poorly understood. Here, we report the 3.51 Å cryo-electron microscopy structure of the TerS from the short-tailed cyanophage Pam5, which infects the host Chao 1806. Pam5 TerS assembles into a nonameric ring with a radially symmetric spiral architecture. Biochemical assays show that Pam5 TerS recognizes the genomic DNA via a specific interaction between the N-terminal helix-turn-helix (HTH) domain of TerS and a 21-bp DNA sequence within the gene. In contrast, the TerS from another short-tailed cyanophage, Pam1, which infects the same host, binds to DNA in a sequence-independent manner. These findings reveal that cyanophages, even infecting the same host, could adopt two distinct DNA recognition strategies: HTH-mediated sequence-dependent or sequence-independent modes. This work provides structural and mechanistic insights into the diverse DNA-recognition strategies of TerS and advances our understanding of the evolutionary plasticity of viral genome packaging mechanisms.
History
DepositionDec 9, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67586.png

Downloads & links

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Map

FileDownload / File: emd_67586.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the cyanophage Pam5 small terminase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 192 pix.
= 205.44 Å		1.07 Å/pix.
x 192 pix.
= 205.44 Å		1.07 Å/pix.
x 192 pix.
= 205.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.426
Minimum - Maximum-1.5849162 - 2.3231993
Average (Standard dev.)-0.0007095634 (±0.051535934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67586_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67586_half_map_2.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 : Pseudanabaena phage Pam5

EntireName: Pseudanabaena phage Pam5 (virus)
Components
  • Virus: Pseudanabaena phage Pam5 (virus)
    • Protein or peptide: Pam5 small terminase

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Supramolecule #1: Pseudanabaena phage Pam5

SupramoleculeName: Pseudanabaena phage Pam5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936521 / Sci species name: Pseudanabaena phage Pam5 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Pam5 small terminase

MacromoleculeName: Pam5 small terminase / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pam5 (virus)
Molecular weightTheoretical: 14.728174 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPALANPRHE RFAQELAKGK SASEAYVAAG YEESRSAASR LSTNVNVQAR VTELQERAAT NVSISREWVL EQLVENARLA KEAGDISPS NQALNLIGKE LGMFVERTEN VNIEHVVSDD LPTAEEWEAE HGTAH

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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 TECNAI F30
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Tecnai F30 / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 906838
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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