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Yorodumi- PDB-7ye6: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ye6 | ||||||
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Title | BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / BAM / BamABCDE / EspP / Gram-negative bacteria / outer membrane protein / outer membrane barrel / BamA / BamB / BamC / BamD / BamE | ||||||
Function / homology | Function and homology information Bam protein complex / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / serine-type endopeptidase activity / response to antibiotic ...Bam protein complex / protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / serine-type endopeptidase activity / response to antibiotic / cell surface / proteolysis / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli O157:H7 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Shen, C. / Chang, S. / Luo, Q. / Zhang, Z. / Luo, B. / Lu, G. / Zhu, X. / Wei, X. / Dong, C. / Zhang, X. ...Shen, C. / Chang, S. / Luo, Q. / Zhang, Z. / Luo, B. / Lu, G. / Zhu, X. / Wei, X. / Dong, C. / Zhang, X. / Tang, X. / Dong, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang ...Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang / Xiaodi Tang / Haohao Dong / Abstract: The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of ...The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials. All known OMPs share the antiparallel β-strand topology, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ye6.cif.gz | 321.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ye6.ent.gz | 253.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ye6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ye6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ye6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7ye6_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 7ye6_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7ye6 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7ye6 | HTTPS FTP |
-Related structure data
Related structure data | 33765MC 7ye4C 8bnzC 8bo2C 7xkl 7yd5 C: citing same article (ref.) M: map data used to model this data |
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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
-Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 90632.422 Da / Num. of mol.: 1 / Mutation: N427C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A940 |
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#2: Protein | Mass: 41918.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamB, yfgL, b2512, JW2496 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P77774 |
#3: Protein | Mass: 36875.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamC, dapX, nlpB, b2477, JW2462 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A903 |
#4: Protein | Mass: 27858.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamD, yfiO, b2595, JW2577 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0AC02 |
#5: Protein | Mass: 13530.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamE, smpA, b2617, JW2598 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A937 |
-Protein , 1 types, 1 molecules P
#6: Protein | Mass: 38684.719 Da / Num. of mol.: 1 / Mutation: R1297C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: espP, L7020, ECO57PM78 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q7BSW5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 7.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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Particle selection | Num. of particles selected: 3723668 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198471 / Symmetry type: POINT |