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- EMDB-21012: A small terminase protein from a thermophilic phage with a fixed ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21012 | |||||||||
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Title | A small terminase protein from a thermophilic phage with a fixed helix-turn-helix geometry, symmetric | |||||||||
![]() | Cryo-EM reconstruction of the thermophilic bacteriophage P74-26 small terminase- symmetric | |||||||||
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![]() | small terminase / bacteriophage / helix-turn-helix / motor / VIRAL PROTEIN | |||||||||
Function / homology | Uncharacterized protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Hayes JA / Hilbert BJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. Authors: Janelle A Hayes / Brendan J Hilbert / Christl Gaubitz / Nicholas P Stone / Brian A Kelch / ![]() Abstract: Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular ...Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerS oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerS revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerS can bind DNA. Finally, the TerS structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerS to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerS, revealing key differences between this thermophilic phage and its mesophilic counterparts. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 75.9 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 49.6 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v1iMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of the thermophilic bacteriophage P74-26 small terminase- symmetric | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 1 of the 9-fold symmetric cryoEM...
File | emd_21012_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of the 9-fold symmetric cryoEM reconstruction of the small terminase protein from the thermophilic bacteriophage P74-26. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the 9-fold symmetric cryoEM...
File | emd_21012_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of the 9-fold symmetric cryoEM reconstruction of the small terminase protein from the thermophilic bacteriophage P74-26. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Gene product 83 of the Thermus thermophilus bacteriophage P74-26
Entire | Name: Gene product 83 of the Thermus thermophilus bacteriophage P74-26 |
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Components |
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-Supramolecule #1: Gene product 83 of the Thermus thermophilus bacteriophage P74-26
Supramolecule | Name: Gene product 83 of the Thermus thermophilus bacteriophage P74-26 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 171 KDa |
-Macromolecule #1: Small terminase protein
Macromolecule | Name: Small terminase protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.080887 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPHMSVSFRD RVLKLYLLGF DPSEIAQTLS LDAKRKVTEE EVLHVLAEAR ELLSALPSLE DIRAEVGQAL ERARIFQKDL LAIYQNMLR NYNAMMEGLT EHPDGTPVIG VRPADIAAMA DRIMKIDQER ITALLNSLKV LGHVGSTTAG ALPSATELVS V EELVAEVA DETPKT UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.4 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: 20 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was monodisperse (PDI= 1.000) |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 2822 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.4000000000000001 µm / Calibrated magnification: 13000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-137 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-6v1i: |