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- EMDB-48906: Azotobacter vinelandii extended type VI secretion system sheath t... -

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Basic information

Entry
Database: EMDB / ID: EMD-48906
TitleAzotobacter vinelandii extended type VI secretion system sheath tube complex
Map data
Sample
  • Complex: Filamentous assembly of the extended type VI secretion system sheath tube complex
    • Protein or peptide: DUF877 family protein
    • Protein or peptide: Type VI secretion system contractile sheath small subunit
  • Ligand: water
Keywordssecretion system / TRANSPORT PROTEIN
Function / homologyType VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system contractile sheath small subunit / DUF877 family protein
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsWarmack RA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: Structure / Year: 2025
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Authors: Yuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack /
Abstract: Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.
History
DepositionFeb 3, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48906.png

Downloads & links

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Map

FileDownload / File: emd_48906.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 864 pix.
= 561.6 Å		0.65 Å/pix.
x 864 pix.
= 561.6 Å		0.65 Å/pix.
x 864 pix.
= 561.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.736
Minimum - Maximum-1.6763479 - 3.2758362
Average (Standard dev.)0.0050095897 (±0.11432121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions864864864
Spacing864864864
CellA=B=C: 561.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48906_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48906_half_map_2.map
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Sample components

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Entire : Filamentous assembly of the extended type VI secretion system she...

EntireName: Filamentous assembly of the extended type VI secretion system sheath tube complex
Components
  • Complex: Filamentous assembly of the extended type VI secretion system sheath tube complex
    • Protein or peptide: DUF877 family protein
    • Protein or peptide: Type VI secretion system contractile sheath small subunit
  • Ligand: water

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Supramolecule #1: Filamentous assembly of the extended type VI secretion system she...

SupramoleculeName: Filamentous assembly of the extended type VI secretion system sheath tube complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: DUF877 family protein

MacromoleculeName: DUF877 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 55.032344 KDa
SequenceString: MAQPSAGETQ ASENITLSLL DRIIAEGRMA HDDSQQDYAR DMLAEFATQV LDEGMAIDKD TVSMINDRIA QIDALIGAQL DEILHHPEL QKLEASWRGL HMLVKNTETG ARLKLRLLNV TQKELLIDLE KAVEFDQSAL FKKIYEEEYG TFGGHPFSLL V GDYSFGRH ...String:
MAQPSAGETQ ASENITLSLL DRIIAEGRMA HDDSQQDYAR DMLAEFATQV LDEGMAIDKD TVSMINDRIA QIDALIGAQL DEILHHPEL QKLEASWRGL HMLVKNTETG ARLKLRLLNV TQKELLIDLE KAVEFDQSAL FKKIYEEEYG TFGGHPFSLL V GDYSFGRH PQDIGLLEKL SNVAAAAHAP FIAAASPRLF DMGSFTELAV PRDLAKIFES QELIKWRAFR ESEDSRYVSL VL PHVLLRL PYGPDTCPVE GMDYVEDVNG RDHARYLWGN AAWALTQRIT EAFARYGWCA AIRGVEGGGA VEGLPAHSFR TSS GDLSLK CPTEVAITDR REKELDALGF IALCHKKNSD LAVFFGSQTT NRPRVYNTNE ANANARISAM LPYVLAASRF AHYL KVIMR DKVGSFMTRD NVQTYLNNWI ADYVLINDNA PQEIKAQYPL REARVDVSEV VGKPGVYRAT VFLRPHFQLE ELTAS IRLV ATLPPPAAA

UniProtKB: DUF877 family protein

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Macromolecule #2: Type VI secretion system contractile sheath small subunit

MacromoleculeName: Type VI secretion system contractile sheath small subunit
type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 20.849465 KDa
SequenceString:
MAESTQHKLD RIRPPRVQIT YDVETGNAIE KKELPLVVGI LADLSGKPEK PLPKLMERRF VEINRDNFND VLASIAPRAA LQVDNTLSQ DGSKLNIELH FDHIDDFDPV NIVRQVTPLR RLFEARQRLR DLLTKLDGND DLDKLLQDVV ANTEGLQEIR S ARPQAENP AGAPGAEPAA DEPAAEPQA

UniProtKB: Type VI secretion system contractile sheath small subunit

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 6150 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: -2.5 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 30.58 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.12 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265571
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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