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- EMDB-4906: Cryo-EM reconstruction of TssA protein from T6SS of Escherichia coli. -

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Basic information

Entry
Database: EMDB / ID: EMD-4906
TitleCryo-EM reconstruction of TssA protein from T6SS of Escherichia coli.
Map data
Sample
  • Complex: C-terminal domain of T6SS protein TssA.
    • Protein or peptide: Putative type VI secretion protein
KeywordsT6SS / E. coli / TssA / cap / transport protein
Function / homologyType VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Putative type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNazarov S / Shneider M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationBSSGI0_155778 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of TssA protein from Type VI secretion system of E. coli.
Authors: Nazarov S / Demurtas D / Shneider M / Basler M / Leiman P
History
DepositionApr 29, 2019-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4906.png

Downloads & links

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Map

FileDownload / File: emd_4906.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 342.792 Å		1.06 Å/pix.
x 324 pix.
= 342.792 Å		1.06 Å/pix.
x 324 pix.
= 342.792 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.02
Minimum - Maximum-0.017939094 - 0.050915625
Average (Standard dev.)-0.000039603594 (±0.0017758003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 342.792 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z342.792342.792342.792
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0180.051-0.000

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Supplemental data

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Mask #1

Fileemd_4906_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_4906_additional_1.map
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Additional map: #2

Fileemd_4906_additional_2.map
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Histogram

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Half map: #2

Fileemd_4906_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4906_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : C-terminal domain of T6SS protein TssA.

EntireName: C-terminal domain of T6SS protein TssA.
Components
  • Complex: C-terminal domain of T6SS protein TssA.
    • Protein or peptide: Putative type VI secretion protein

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Supramolecule #1: C-terminal domain of T6SS protein TssA.

SupramoleculeName: C-terminal domain of T6SS protein TssA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 634 KDa

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Macromolecule #1: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 59.159789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASIHSLLSA CQTTPRDVAE PAQVRIALWD KWLAPVTPDN PAGDDAGYDD DFQQMREEVN KLSGADAGIV SQLAEKLLTT RTKDIRVAT WYIWARLRQD GEKGLADGLE LLTGLLQRFG EHLHPQRSRA RKAALEWLCS ARILDSLSLY PEVVKADTLR I AGALWLAE ...String:
MASIHSLLSA CQTTPRDVAE PAQVRIALWD KWLAPVTPDN PAGDDAGYDD DFQQMREEVN KLSGADAGIV SQLAEKLLTT RTKDIRVAT WYIWARLRQD GEKGLADGLE LLTGLLQRFG EHLHPQRSRA RKAALEWLCS ARILDSLSLY PEVVKADTLR I AGALWLAE QTFTDEASAP VLNGLYQALE NRLMKAGGVD AVVPQEAAAP APTVTSGSVM ALSAITSGQE LLSQARVLAK YL RDQPEGW LAAHRLMKSV RHDTLHQLPP LSADGRTRIA PPGPDRRASL KRLYLQQNWL SLLEQCDDMF ARGASHLWLD LQW YIHQAL LQTGKENYAA IIQYDLKGLL LRLPGLETLA FNDGMPFADD VTLSWIQQQV MECGERWAEE PSVTITAAPG DNDI LSLEP EALQIADNEG TEAALSWLQA RPGIQSDRSN WLLRLL(MSE)ARV AEQTGKNDLA LHLLAELDER ATRLTLSQWE P ELVFEVKA RRLKLLR(MSE)KS AKTESDRVRL QPD(MSE)EHLLAG LIAIDAARAA VLCNSGSS

UniProtKB: Putative type VI secretion 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 / Chamber humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3269 / 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 / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 667861
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 52370
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4yo5


Chain - Chain ID: A / Chain - Residue range: 388-474 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6rju:
C-terminal domain of TssA protein from T6SS of Escherichia coli.

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