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- EMDB-16770: Type II Secretion System -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16770
TitleType II Secretion System
Map datamap
Sample
  • Complex: Type II Secretion System
    • Protein or peptide: Probable type IV piliation system protein DR_0774
    • Protein or peptide: IPT/TIG domain-containing protein
    • Protein or peptide: Lipoprotein
KeywordsType II Secretion System / MEMBRANE PROTEIN / Cell envelope
Function / homology
Function and homology information


type II protein secretion system complex / cell envelope / protein secretion
Similarity search - Function
: / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / IPT/TIG domain / IPT domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
IPT/TIG domain-containing protein / Lipoprotein / Probable type IV piliation system protein DR_0774
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant) / Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsFarci D / Piano D
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2018/30/M/NZ1/00284 Poland
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
CitationJournal: J Biol Chem / Year: 2024
Title: Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans.
Authors: Domenica Farci / Stefan Milenkovic / Luca Iesu / Marta Tanas / Matteo Ceccarelli / Dario Piano /
Abstract: The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) ...The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.
History
DepositionFeb 26, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16770.png

Downloads & links

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Map

FileDownload / File: emd_16770.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 500 pix.
= 600. Å		1.2 Å/pix.
x 500 pix.
= 600. Å		1.2 Å/pix.
x 500 pix.
= 600. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-4.9081664 - 6.503895
Average (Standard dev.)0.0043500853 (±0.104786344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B; same hand as primary map

Fileemd_16770_half_map_1.map
Annotationhalf map B; same hand as primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A; same hand as primary map

Fileemd_16770_half_map_2.map
Annotationhalf map A; same hand as primary 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

EntireName: Type II Secretion System
Components
  • Complex: Type II Secretion System
    • Protein or peptide: Probable type IV piliation system protein DR_0774
    • Protein or peptide: IPT/TIG domain-containing protein
    • Protein or peptide: Lipoprotein

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Supramolecule #1: Type II Secretion System

SupramoleculeName: Type II Secretion System / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: Probable type IV piliation system protein DR_0774

MacromoleculeName: Probable type IV piliation system protein DR_0774 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Molecular weightTheoretical: 78.653461 KDa
SequenceString: MNKRHALLLT AVLGMATAYA QTAPTTTTVN TLQTVYRDPS LTSAPITANV GKYVGPLSTF LASIAKSAGY EVVFNFNIDA LALINGEIV FGNSTASVTT SYATPLGRPQ ELPAKPVVHN FSNAPFNEAW PLLMDVYELD YQLVKVGSAN VIRIGQRPKQ L ALPLKFIS ...String:
MNKRHALLLT AVLGMATAYA QTAPTTTTVN TLQTVYRDPS LTSAPITANV GKYVGPLSTF LASIAKSAGY EVVFNFNIDA LALINGEIV FGNSTASVTT SYATPLGRPQ ELPAKPVVHN FSNAPFNEAW PLLMDVYELD YQLVKVGSAN VIRIGQRPKQ L ALPLKFIS AESALTAIEK FFGEEKFETV ISLDSNNKPF QTTRPTGKFG LPNSIKVIPD SSNKRLIIGS NSEDGIRIRS FV ETIDVQS SGKVISTDSI SEIYIVRGQK ESVLQFLRDS FPELIVTDYA SGGLAIEGPR TSVNRAIILL GQVDRAPEIP IVQ RIYTVR GQAADITALL AAQYPTLRVT PVGQTGQLVL NGAQAQLDTA LALLEQVDRP APVAESRTVQ RVFQLVNASA EEVK ATLEG TLARDLTADS NNDVLPNVPV TATDANGNTT VVSVPNALGK TANQGTANAQ AQTAQTPANT QQATLIADKR TNSLI VRGT PEQVAQVAEL VPQLDQVVPQ INVQVRIQEV NERALQSLGL NWRATFGGFN VAVSGGTGLA ATFNPTQSFL GFNIFP TLT ALETQGLTRR VYDGNVTMQS GQRSLSATGG AQNASSGAAA SVKSGGRLEI NIPSAAGNIV RQIDYGLNLD FFSPQVA PD GTITLRIRGQ VNQPATAITA DSLPNLIDFT NSEAQSTITF KNGQTILMSG LLGSTETTNR SGVPFLSSLP GVGAAFGE K RTEKTQSQLL VIITGTVVK

UniProtKB: Probable type IV piliation system protein DR_0774

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Macromolecule #2: IPT/TIG domain-containing protein

MacromoleculeName: IPT/TIG domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Molecular weightTheoretical: 15.954317 KDa
SequenceString:
MTALGVEHDQ HPACGGGSLT RHLQLIRLPG GGLSMLRFFC ASLLLTGLLA SCTPRVTTVA GVTVTPVLIK VSEGAAPGDT LTIQGRYLG NAQTARVIIG ADENGQGGTA FPASAVQSWS DTEIVLKVPE GMPAGGSWLF VEVGGKRSTG LRVSVR

UniProtKB: IPT/TIG domain-containing protein

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Macromolecule #3: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Molecular weightTheoretical: 21.814654 KDa
SequenceString: MTMKKMFPVL LLGGLLLAGC GTVGLGSGRV NVGVDVGDAG SEQVATLTIT PEKCDDKGVC TPQKQELSIT DGQPVTFTFT ARPGSEAVT IEGYRVLSDR LDGVERADPK NPVENAKMNL YVPSGYACEG LTAGASCQGN ESDIRIANGQ PVQHQIYFAS G LGARAAAK ...String:
MTMKKMFPVL LLGGLLLAGC GTVGLGSGRV NVGVDVGDAG SEQVATLTIT PEKCDDKGVC TPQKQELSIT DGQPVTFTFT ARPGSEAVT IEGYRVLSDR LDGVERADPK NPVENAKMNL YVPSGYACEG LTAGASCQGN ESDIRIANGQ PVQHQIYFAS G LGARAAAK GANVTRVVDL EFYGFSANNV PFTRKVTGIV SQGSYVVKTN

UniProtKB: Lipoprotein

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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