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- PDB-6lyu: Structure of the BAM complex -

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Basic information

Entry
Database: PDB / ID: 6lyu
TitleStructure of the BAM complex
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamB
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsMEMBRANE PROTEIN / b-barrel assembly machinery (BAM) complex
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane
Similarity search - Function
PQQ enzyme repeat / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like ...PQQ enzyme repeat / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Pyrrolo-quinoline quinone beta-propeller repeat / Omp85 superfamily domain / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsXiao, L. / Huang, Y.
CitationJournal: FASEB J / Year: 2021
Title: Structures of the β-barrel assembly machine recognizing outer membrane protein substrates.
Authors: Le Xiao / Long Han / Bufan Li / Manfeng Zhang / Haizhen Zhou / Qingshan Luo / Xinzheng Zhang / Yihua Huang /
Abstract: β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative ...β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery (BAM) complex, yet its precise mechanism remains elusive. Here, we report two structures of the BAM complex in detergents and in nanodisks, and two crystal structures of the BAM complex with bound substrates. Structural analysis indicates that the membrane compositions surrounding the BAM complex could modulate its overall conformations, indicating low energy barriers between different conformational states and a highly dynamic nature of the BAM complex. Importantly, structures of the BAM complex with bound substrates and the related functional analysis show that the first β-strand of the BamA β-barrel (β1 ) in the BAM complex is associated with the last but not the first β-strand of a β-OMP substrate via antiparallel β-strand interactions. These observations are consistent with the β-signal hypothesis during β-OMP biogenesis, and suggest that the β1 strand in the BAM complex may interact with the last β-strand of an incoming β-OMP substrate upon their release from the chaperone-bound state.
History
DepositionFeb 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)211,4785
Polymers211,4785
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 90643.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamB


Mass: 42961.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 36875.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 27858.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AC02
#5: Protein Outer membrane protein assembly factor BamE


Mass: 13139.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A937

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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: B-barrel assembly machinery (BAM) complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: SerialEM / Version: 3.7 / Category: image acquisition / Details: collect data
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395915 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00812065
ELECTRON MICROSCOPYf_angle_d0.96216402
ELECTRON MICROSCOPYf_dihedral_angle_d8.351663
ELECTRON MICROSCOPYf_chiral_restr0.0511799
ELECTRON MICROSCOPYf_plane_restr0.0062164

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