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Yorodumi- PDB-8bo2: BAM-EspP complex structure with BamA-S425C/EspP-S1299C mutations ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bo2 | ||||||
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Title | BAM-EspP complex structure with BamA-S425C/EspP-S1299C mutations in nanodisc | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / BAM / BamABCDE / EspP / Gram-negative bacteria / outer membrane protein / outer membrane barrel / BamA / BamB / BamC / BamD / BamE / MEMBRANE PROTEIN / Outer membrane protein insertion and release | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / response to antibiotic / serine-type endopeptidase activity / cell surface ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / response to antibiotic / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Shen, C. / Chang, S. / Luo, Q. / Zhang, Z. / Xie, T. / Luo, B. / Lu, G. / Zhu, X. / Wei, X. / Dong, C. ...Shen, C. / Chang, S. / Luo, Q. / Zhang, Z. / Xie, T. / Luo, B. / Lu, G. / Zhu, X. / Wei, X. / Dong, C. / Zhou, R. / 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 | 8bo2.cif.gz | 297.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bo2.ent.gz | 215.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bo2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8bo2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bo2_validation.xml.gz | 54.3 KB | Display | |
Data in CIF | 8bo2_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8bo2 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8bo2 | HTTPS FTP |
-Related structure data
Related structure data | 16138MC 7ye4C 7ye6C 8bnzC 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
-Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 88273.555 Da / Num. of mol.: 1 / Mutation: S425C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / DH10B / Gene: bamA, yaeT, ECDH10B_0157 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B1XD46 |
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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: 38754.836 Da / Num. of mol.: 1 / Mutation: S1299C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (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 (recombinant) |
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Buffer solution | pH: 7.8 | ||||||||||||||||||||||||
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203494 / Symmetry type: POINT | |||||||||
Refinement | Cross valid method: NONE |