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- PDB-7ye4: BAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ye4 | ||||||
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Title | BAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc | ||||||
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![]() | MEMBRANE PROTEIN / BAM / BamABCDE / EspP / Gram-negative bacteria / outer membrane protein / outer membrane barrel / BamA / BamB / BamC / BamD / BamE | ||||||
Function / homology | ![]() 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 / cell adhesion / response to antibiotic / serine-type endopeptidase activity ...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 / cell adhesion / response to antibiotic / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 323.6 KB | Display | ![]() |
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PDB format | ![]() | 255 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 33763MC ![]() 7ye6C ![]() 8bnzC ![]() 8bo2C ![]() 7xkl ![]() 7yd5 M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 90735.562 Da / Num. of mol.: 1 / Mutation: G431C,G781C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() 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.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P77774 |
#3: Protein | Mass: 36875.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0A903 |
#4: Protein | Mass: 27858.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0AC02 |
#5: Protein | Mass: 13530.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0A937 |
-Protein , 1 types, 1 molecules P
#6: Protein | Mass: 38759.879 Da / Num. of mol.: 1 / Mutation: N1293C, A1043C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() 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 |
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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-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
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) |
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Processing
CTF correction | Type: NONE |
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Particle selection | Num. of particles selected: 2315966 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142423 / Symmetry type: POINT |
Atomic model building | B value: 100 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: 0.3 |
Atomic model building | PDB-ID: 7YD5![]() 7yd5 Accession code: 7YD5 / Source name: PDB / Type: experimental model |