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- EMDB-65926: Cryo-EM structure of the Type II secretion system protein from Ac... -

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Basic information

Entry
Database: EMDB / ID: EMD-65926
TitleCryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
Map data
Sample
  • Complex: Type II secretion system protein
    • Protein or peptide: Type II and III secretion system protein
Keywords--Type II secretion system protein / Acidithiobacillus caldus / TOXIN
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 (strain SM-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsLiu RH / Zhang K / Feng QS / Dai X / Zhang X / Li W / Bao ZP / Lin WF / Fu Y / Li Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Funct Mater / Year: 2025
Title: Unveiling Acidophilic Secretin Nanopores for Ion Exclusion and Single-Molecule Sensing
Authors: Liu R / Zhang K / Feng Q / He S / Fan Q / Zhang X / Li W / Bao Z / Lin W / Fu Y / Li Y
History
DepositionAug 21, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65926.png

Downloads & links

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Map

FileDownload / File: emd_65926.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å		0.67 Å/pix.
x 480 pix.
= 320.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.19015805 - 0.40021825
Average (Standard dev.)0.00006361412 (±0.014109086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 320.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65926_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65926_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type II secretion system protein

EntireName: Type II secretion system protein
Components
  • Complex: Type II secretion system protein
    • Protein or peptide: Type II and III secretion system protein

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Supramolecule #1: Type II secretion system protein

SupramoleculeName: Type II secretion system protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acidithiobacillus caldus (strain SM-1) (bacteria)

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Macromolecule #1: Type II and III secretion system protein

MacromoleculeName: Type II and III secretion system protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Acidithiobacillus caldus (strain SM-1) (bacteria)
Molecular weightTheoretical: 53.556238 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLRGKILPL FVAIAMAIPA QAAEDRTIDL YAGQVRVIPT KPVKRVAIGD GKVLSTTVVD GNELLLLGDA EGETSLRVWF KDGSEAAYR VLVAPKNVGR AAEEMRELMG AEKSPAKIRV VGDHVVVDGK NLAPTTLARV RALQALYPKT IVLATPSPFD M EKMVWLDV ...String:
MKLRGKILPL FVAIAMAIPA QAAEDRTIDL YAGQVRVIPT KPVKRVAIGD GKVLSTTVVD GNELLLLGDA EGETSLRVWF KDGSEAAYR VLVAPKNVGR AAEEMRELMG AEKSPAKIRV VGDHVVVDGK NLAPTTLARV RALQALYPKT IVLATPSPFD M EKMVWLDV NILEIRKSVL ENFGVDWSKQ IPGPFAAFGK DFVGPRNVAT IPLGQDLTQP PVAGTGVRVT PPLGSLNGAI DL ANLARPI AGTTNFGIIT GVLSTINFAL SNGDAYLIAN PQLSARSGGR TDFLAGGQVP ILQALAAGNA AFQNVTYKDY GIK LEFEPR VDDDNNVSMR VLADVSDIDP ATSVSLNGFT VPGFITRRSN AEINVGDGQT MVISGLVNPK TAKNVSKLPW LGDI PILGN LFKSTNFQSG NTDLVILVTP RVVSAASLEN IRQVSQAVEM KDEYRNTLPK GSTTRDAVDR TLGSKTPYPE TQAVP APKP SLPLVVTQPP AAMPSDKE

UniProtKB: Type II and III secretion system 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

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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: 3.2 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 452989
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72834
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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