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

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Basic information

Entry
Database: PDB / ID: 6lyr
TitleStructure of the BAM complex
Components
  • (Outer membrane protein assembly factor ...) x 5
  • Peptide from Outer membrane protein A
KeywordsMEMBRANE PROTEIN / b-barrel assembly machinery (BAM) complex
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / porin activity / pore complex / protein insertion into membrane / monoatomic ion transport ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / porin activity / pore complex / protein insertion into membrane / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / DNA damage response / symbiont entry into host cell / cell surface / identical protein binding / membrane
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Outer membrane protein, bacterial / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Outer membrane protein, bacterial / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / BamE-like / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein A / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsXiao, L. / Huang, Y.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Structure of the BAM complex
Authors: Xiao, L. / Huang, Y.
History
DepositionFeb 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
P: Peptide from Outer membrane protein A


Theoretical massNumber of molelcules
Total (without water)212,3786
Polymers212,3786
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-75 kcal/mol
Surface area64830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.877, 116.877, 430.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE

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


Mass: 90666.422 Da / Num. of mol.: 1
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 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 K-12 (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 K-12 (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 K-12 (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 K-12 (bacteria) / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A937

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Protein/peptide , 1 types, 1 molecules P

#6: Protein/peptide Peptide from Outer membrane protein A / OmpA / Outer membrane porin A / Outer membrane protein 3A / Outer membrane protein B / Outer ...OmpA / Outer membrane porin A / Outer membrane protein 3A / Outer membrane protein B / Outer membrane protein II* / Outer membrane protein d


Mass: 877.019 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ompA, con, tolG, tut, b0957, JW0940 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A910

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 27-30% PEG 400, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.28→50 Å / Num. obs: 44370 / % possible obs: 99.6 % / Redundancy: 18.7 % / CC1/2: 1 / Net I/σ(I): 16.5
Reflection shellResolution: 3.28→3.36 Å / Num. unique obs: 3160 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D0O

5d0o


Resolution: 3.28→49.37 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.906 / SU B: 24.069 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 2302 4.9 %RANDOM
Rwork0.2465 ---
obs0.2482 44370 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 195.97 Å2 / Biso mean: 95.812 Å2 / Biso min: 65.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2--3.68 Å2-0 Å2
3----7.37 Å2
Refinement stepCycle: final / Resolution: 3.28→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 0 0 11439
Num. residues----1503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01311681
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710391
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.63915913
X-RAY DIFFRACTIONr_angle_other_deg1.1491.57524056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69451493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18923.196607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98151758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3531562
X-RAY DIFFRACTIONr_chiral_restr0.0450.21521
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213438
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022464
LS refinement shellResolution: 3.28→3.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 151 -
Rwork0.335 3160 -
all-3311 -
obs--97.5 %

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