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- PDB-9n4v: Azotobacter vinelandii extended type VI secretion system sheath t... -

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Basic information

Entry
Database: PDB / ID: 9n4v
TitleAzotobacter vinelandii extended type VI secretion system sheath tube complex
Components
  • DUF877 family protein
  • Type VI secretion system contractile sheath small subunit
KeywordsTRANSPORT PROTEIN / secretion system
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsWarmack, R.A.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Sep 17, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF877 family protein
B: Type VI secretion system contractile sheath small subunit
C: DUF877 family protein
D: Type VI secretion system contractile sheath small subunit
E: DUF877 family protein
F: Type VI secretion system contractile sheath small subunit
G: DUF877 family protein
H: Type VI secretion system contractile sheath small subunit
I: DUF877 family protein
J: Type VI secretion system contractile sheath small subunit
K: DUF877 family protein
L: Type VI secretion system contractile sheath small subunit
M: DUF877 family protein
N: Type VI secretion system contractile sheath small subunit
O: DUF877 family protein
P: Type VI secretion system contractile sheath small subunit
Q: DUF877 family protein
R: Type VI secretion system contractile sheath small subunit
S: DUF877 family protein
T: Type VI secretion system contractile sheath small subunit
U: DUF877 family protein
V: Type VI secretion system contractile sheath small subunit
W: DUF877 family protein
X: Type VI secretion system contractile sheath small subunit
Y: DUF877 family protein
Z: Type VI secretion system contractile sheath small subunit
a: DUF877 family protein
b: Type VI secretion system contractile sheath small subunit
c: DUF877 family protein
d: Type VI secretion system contractile sheath small subunit
e: DUF877 family protein
f: Type VI secretion system contractile sheath small subunit
g: DUF877 family protein
h: Type VI secretion system contractile sheath small subunit
i: DUF877 family protein
j: Type VI secretion system contractile sheath small subunit
k: DUF877 family protein
l: Type VI secretion system contractile sheath small subunit
m: DUF877 family protein
n: Type VI secretion system contractile sheath small subunit
o: DUF877 family protein
p: Type VI secretion system contractile sheath small subunit
q: DUF877 family protein
r: Type VI secretion system contractile sheath small subunit
s: DUF877 family protein
t: Type VI secretion system contractile sheath small subunit
u: DUF877 family protein
v: Type VI secretion system contractile sheath small subunit


Theoretical massNumber of molelcules
Total (without water)1,821,16348
Polymers1,821,16348
Non-polymers00
Water110,7926150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
DUF877 family protein


Mass: 55032.344 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: C1DM91
#2: Protein ...
Type VI secretion system contractile sheath small subunit


Mass: 20849.465 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: C1DM90
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filamentous assembly of the extended type VI secretion system sheath tube complex
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 22.12 ° / Axial rise/subunit: 30.58 Å / Axial symmetry: C6
3D reconstructionResolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265571 / Symmetry type: HELICAL
RefinementHighest resolution: 1.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00483664
ELECTRON MICROSCOPYf_angle_d0.609113352
ELECTRON MICROSCOPYf_dihedral_angle_d4.70611280
ELECTRON MICROSCOPYf_chiral_restr0.04112672
ELECTRON MICROSCOPYf_plane_restr0.00514664

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