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- PDB-8jvb: Cryo-EM structure of the Type II secretion system protein from Ac... -

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Basic information

Entry
Database: PDB / ID: 8jvb
TitleCryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
ComponentsType II and III secretion system protein
KeywordsTOXIN / Type II secretion system protein / Acidithiobacillus caldus
Function / homologyPilus formation protein, N-terminal / Pilus formation protein N terminal region / GspD/PilQ family / : / Type II/III secretion system / Bacterial type II and III secretion system protein / type II protein secretion system complex / protein secretion / Type II and III secretion system protein
Function and homology information
Biological speciesAcidithiobacillus caldus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsLiu, R.H. / Zhang, K. / Feng, Q.S. / Dai, X. / Fu, Y. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
Authors: Zhang, K.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II and III secretion system protein
B: Type II and III secretion system protein
C: Type II and III secretion system protein
D: Type II and III secretion system protein
E: Type II and III secretion system protein
F: Type II and III secretion system protein
G: Type II and III secretion system protein
H: Type II and III secretion system protein
I: Type II and III secretion system protein
J: Type II and III secretion system protein
K: Type II and III secretion system protein
L: Type II and III secretion system protein
M: Type II and III secretion system protein
N: Type II and III secretion system protein


Theoretical massNumber of molelcules
Total (without water)749,78714
Polymers749,78714
Non-polymers00
Water00
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
Type II and III secretion system protein


Mass: 53556.238 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus caldus (strain SM-1) (bacteria)
Gene: Atc_2749 / Production host: Escherichia coli B (bacteria) / References: UniProt: F9ZTP9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Type II secretion system protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Acidithiobacillus caldus (strain SM-1) (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 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 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72834 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338906
ELECTRON MICROSCOPYf_angle_d0.56852962
ELECTRON MICROSCOPYf_dihedral_angle_d5.135404
ELECTRON MICROSCOPYf_chiral_restr0.0456314
ELECTRON MICROSCOPYf_plane_restr0.0066958

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