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- EMDB-48918: CryoEM structure of the Azotobacter vinelandii flagellar filament -

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Basic information

Entry
Database: EMDB / ID: EMD-48918
TitleCryoEM structure of the Azotobacter vinelandii flagellar filament
Map data
Sample
  • Complex: Filamentous assembly of the Azotobacter vinelandii flagellar filament
    • Protein or peptide: Flagellin
KeywordsFlagellum / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, H7-serospecific domain / Flagellin protein / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesAzotobacter vinelandii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.82 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-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48918.png

Downloads & links

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Map

FileDownload / File: emd_48918.map.gz / Format: CCP4 / Size: 3.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 980 pix.
= 637. Å		0.65 Å/pix.
x 980 pix.
= 637. Å		0.65 Å/pix.
x 980 pix.
= 637. 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: 0.17
Minimum - Maximum-0.4090774 - 0.8251137
Average (Standard dev.)0.0006232554 (±0.029966386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions980980980
Spacing980980980
CellA=B=C: 637.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48918_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_48918_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Filamentous assembly of the Azotobacter vinelandii flagellar filament

EntireName: Filamentous assembly of the Azotobacter vinelandii flagellar filament
Components
  • Complex: Filamentous assembly of the Azotobacter vinelandii flagellar filament
    • Protein or peptide: Flagellin

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Supramolecule #1: Filamentous assembly of the Azotobacter vinelandii flagellar filament

SupramoleculeName: Filamentous assembly of the Azotobacter vinelandii flagellar filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 58.040414 KDa
SequenceString: MPVINTNITS LIAQKNLSSS QSALTTAMER LSSGMRINSA KDDAAGQAIA NRMSSQITGL TQAQRNANDG ISVAQTTEGA LDQINDNLQ RIRELTVQAQ NGTNSSEDLT SIQNEIAQRL DEIDRISQET EFNGVKVLSK DTNLNIQVGA NDGQSIGISL K QINAKTLG ...String:
MPVINTNITS LIAQKNLSSS QSALTTAMER LSSGMRINSA KDDAAGQAIA NRMSSQITGL TQAQRNANDG ISVAQTTEGA LDQINDNLQ RIRELTVQAQ NGTNSSEDLT SIQNEIAQRL DEIDRISQET EFNGVKVLSK DTNLNIQVGA NDGQSIGISL K QINAKTLG LDGFNVDGSG ATQNSTATVT SLEGAGAVKN STTGNYVLTT TFDEASLERM LGEMKDGDVV TVGSGASTAV EY TFNTASG SFTYTANATN AAAYGDLADE LIPPTGSSIT GTYEFADGNV ATFAVDASGK LTLDGQAAYV TATGELTNNA TSG ATQATL EDLFATVGAG AAGTDTSARS LTVGGVTYTG AGTTAGLSYT DTATSSDVLA ASASTVASIE MHNGITSATI DFDN TGAQS STGTQVYVDE DGQLTTVGSY TTTFAVNADT GEVTVVDNSD TAGDYALEEG ATVYVGSNGR LTTSTTSKGD VTEDP LAAL DAALASVDAL RSDLGAIQNR FDSAINNLST TTTNLSAARS RIEDADYAVE VANMTKAQIL QQAGTSVLAQ ANQVPQ SVL SLLG

UniProtKB: Flagellin

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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: 9.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 130.80 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47453
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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