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- EMDB-51565: Cryo-EM structure of a contractile injection system in Streptomyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-51565
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 3-fold symmetry.
Map data
Sample
  • Complex: The baseplate module applied 3-fold symmetry of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Gp5/Type VI secretion system Vgr protein OB-fold domain-containing protein
KeywordsContractile injection system / STRUCTURAL PROTEIN
Function / homology: / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Gp5/Type VI secretion system Vgr protein OB-fold domain-containing protein
Function and homology information
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsCasu B / Sallmen JW / Hass PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 Switzerland
European Research Council (ERC)679209European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015349/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
CitationJournal: To Be Published
Title: Firing and cellular function of the Streptomyces coelicolor contractile injection system require the membrane protein CisA
Authors: Casu B / Sallmen JW / Hass PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
History
DepositionSep 18, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51565.png

Downloads & links

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Map

FileDownload / File: emd_51565.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0092
Minimum - Maximum-0.013382614 - 0.033291966
Average (Standard dev.)0.0002533315 (±0.0029691095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 447.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51565_msk_1.map
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Half map: #1

Fileemd_51565_half_map_1.map
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Half map: #2

Fileemd_51565_half_map_2.map
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Sample components

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Entire : The baseplate module applied 3-fold symmetry of a contractile inj...

EntireName: The baseplate module applied 3-fold symmetry of a contractile injection system in Streptomyces coelicolor
Components
  • Complex: The baseplate module applied 3-fold symmetry of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Gp5/Type VI secretion system Vgr protein OB-fold domain-containing protein

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Supramolecule #1: The baseplate module applied 3-fold symmetry of a contractile inj...

SupramoleculeName: The baseplate module applied 3-fold symmetry of a contractile injection system in Streptomyces coelicolor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)

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Macromolecule #1: Gp5/Type VI secretion system Vgr protein OB-fold domain-containin...

MacromoleculeName: Gp5/Type VI secretion system Vgr protein OB-fold domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 68.161953 KDa
SequenceString: MVRPSFSSIV EVKIGGAKLP DTIAPMLTDG WVDQGVNVPA AFRLTFRDPY HRLLGDLNVQ FGTKVVITPI ADGQGKNNPL LTGEVTGLE TDYDGTGSFT VIRGYDYGHR LMRQRRVAAY RNQKASDIAR KLVQMDGVSV GRIQPTKGTY AFIAQPNVTD W DFLARLAD ...String:
MVRPSFSSIV EVKIGGAKLP DTIAPMLTDG WVDQGVNVPA AFRLTFRDPY HRLLGDLNVQ FGTKVVITPI ADGQGKNNPL LTGEVTGLE TDYDGTGSFT VIRGYDYGHR LMRQRRVAAY RNQKASDIAR KLVQMDGVSV GRIQPTKGTY AFIAQPNVTD W DFLARLAD ENKMIMYLDS KGKFRFVTPK PSAGAPSPNT DGDQSAFVLQ AGHDILRLRA AVTAADQIGK VESRGWNVTT KK KITEIAP ATTDPGISIK WTPGTAAGKF KPGKLVETAN PYDKQDEVQN AAKALASDVT ASFSELEVAA NGHPDLRPGV PVA LSDVGT PFEGKYTVTS VRHHFGDGVA YESWITVSGR QWRSLYGLAS GGGGSDPASA TRLPSVANAI VTDVQDPLKQ GRVK LQFPW LDDTYVSDWA RSVQMGGVAG GGIFPMDVGD EVLVAFDRGA LDHPFVIGGL YNGRDVPTKS DVPLHDGLKK KAVRH TLSD RQGNRVDLLS QRTGGRKQGV RIASGNDKLT INLDRTKTEI TVDSKGSVSI TGSRSVSVDA GTDLSLSARR SLTIKS GGP LSIQGGSTIN MRSGGLVGVN AGGALNLGAG GAATLSAGAA TTISGTVNVQ INSVMTRVIG ATFEVKTPIF KVATIPV PG L

UniProtKB: Gp5/Type VI secretion system Vgr protein OB-fold 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: 8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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