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Yorodumi- PDB-8gra: Structure of Type VI secretion system cargo delivery vehicle Hcp-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gra | ||||||
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Title | Structure of Type VI secretion system cargo delivery vehicle Hcp-VgrG-PAAR | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Type VI Secretion System / VgrG / Hcp5 / PAAR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Wen, Y. / He, W. / Zhu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Rep / Year: 2023 Title: Structure and assembly of type VI secretion system cargo delivery vehicle. Authors: Wenbo He / Ke Wu / Zhenlin Ouyang / Yixin Bai / Wen Luo / Di Wu / Hao An / Yucheng Guo / Min Jiao / Qian Qin / Jiaxin Zhang / Yi Wu / Junjun She / Peter M Hwang / Fang Zheng / Li Zhu / Yurong Wen / Abstract: Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS ...Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gra.cif.gz | 500.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gra.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8gra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gra_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8gra_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8gra_validation.xml.gz | 84.9 KB | Display | |
Data in CIF | 8gra_validation.cif.gz | 128 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/8gra ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8gra | HTTPS FTP |
-Related structure data
Related structure data | 34087MC 7yw0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 23725.367 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: DXA78_05585, F2Z89_01155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E5IG32 #2: Protein | Mass: 14505.281 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) Gene: tssD_4, CQW34_01545, DW228_07065, DWW08_15770, EC81_0218805, F2Z25_09975, F2Z89_01225, F9000_04115, FSA06_12535, H3T27_02635, HMPREF0101_00911, HMPREF1018_02079, IB64_010900 Production host: Escherichia coli (E. coli) / References: UniProt: A0A081TQ32 #3: Protein | Mass: 67969.055 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: DXA78_05580, F2Z89_01160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E5IG38 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hcp-VgrG-PAAR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4300 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354265 / Symmetry type: POINT | ||||||||||||||||||||||||
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