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- PDB-8co1: Type II Secretion System -

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Basic information

Entry
Database: PDB / ID: 8co1
TitleType II Secretion System
Components
  • IPT/TIG domain-containing protein
  • Lipoprotein
  • Probable type IV piliation system protein DR_0774
KeywordsMEMBRANE PROTEIN / Type II Secretion System / Cell envelope
Function / homology
Function and homology information


: / type II protein secretion system complex / protein secretion
Similarity search - Function
NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / 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 = ATCC 13939 = DSM 20539 (radioresistant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsFarci, D. / Piano, D.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2018/30/M/NZ1/00284 Poland
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
Citation
Journal: 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.
#1: Journal: 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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q1: Probable type IV piliation system protein DR_0774
Q2: IPT/TIG domain-containing protein
Q3: Lipoprotein
P1: Probable type IV piliation system protein DR_0774
P2: IPT/TIG domain-containing protein
P3: Lipoprotein
O1: Probable type IV piliation system protein DR_0774
O2: IPT/TIG domain-containing protein
O3: Lipoprotein
N1: Probable type IV piliation system protein DR_0774
N2: IPT/TIG domain-containing protein
N3: Lipoprotein
M1: Probable type IV piliation system protein DR_0774
M2: IPT/TIG domain-containing protein
M3: Lipoprotein
L1: Probable type IV piliation system protein DR_0774
L2: IPT/TIG domain-containing protein
L3: Lipoprotein
A1: Probable type IV piliation system protein DR_0774
A2: IPT/TIG domain-containing protein
A3: Lipoprotein
I1: Probable type IV piliation system protein DR_0774
I2: IPT/TIG domain-containing protein
I3: Lipoprotein
H1: Probable type IV piliation system protein DR_0774
H2: IPT/TIG domain-containing protein
H3: Lipoprotein
F1: Probable type IV piliation system protein DR_0774
F2: IPT/TIG domain-containing protein
F3: Lipoprotein
G1: Probable type IV piliation system protein DR_0774
G2: IPT/TIG domain-containing protein
G3: Lipoprotein
E1: Probable type IV piliation system protein DR_0774
E2: IPT/TIG domain-containing protein
E3: Lipoprotein
D1: Probable type IV piliation system protein DR_0774
D2: IPT/TIG domain-containing protein
D3: Lipoprotein
C1: Probable type IV piliation system protein DR_0774
C2: IPT/TIG domain-containing protein
C3: Lipoprotein
B1: Probable type IV piliation system protein DR_0774
B2: IPT/TIG domain-containing protein
B3: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)1,746,33645
Polymers1,746,33645
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area270340 Å2
ΔGint-990 kcal/mol
Surface area547630 Å2

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Components

#1: Protein
Probable type IV piliation system protein DR_0774


Mass: 78653.461 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
References: UniProt: Q9RW95
#2: Protein
IPT/TIG domain-containing protein


Mass: 15954.317 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
References: UniProt: Q9RUM0
#3: Protein
Lipoprotein


Mass: 21814.654 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
References: UniProt: Q9RVT2

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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 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Buffer solutionpH: 7
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00796177
ELECTRON MICROSCOPYf_angle_d0.691130841
ELECTRON MICROSCOPYf_dihedral_angle_d14.51313515
ELECTRON MICROSCOPYf_chiral_restr0.0515554
ELECTRON MICROSCOPYf_plane_restr0.00517235

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