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- EMDB-51930: BAM-hinge (LVPR) -

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Basic information

Entry
Database: EMDB / ID: EMD-51930
TitleBAM-hinge (LVPR)
Map dataE. coli BAM with LVPR insertion in POTRA-barrel domain linker region.
Sample
  • Complex: BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamC
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE
KeywordsOuter membrane / folding / OMP / MEMBRANE PROTEIN
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 / cell surface / identical protein binding / membrane
Similarity search - Function
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 / 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 protein assembly factor BamB / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / 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 / 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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMachin JM / Ranson NA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust222373/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/Y012453/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Molecular insights into how the motions of the β-barrel and POTRA domains of BamA are coupled for efficient function.
Authors: Naemi Csoma / Jonathan M Machin / James M Whitehouse / Raquel Rodrìguez-Alonso / Monika Olejnik / Adam K Cahill / Seung-Hyun Cho / Till F Schäberle / Bogdan I Iorga / Neil A Ranson / ...Authors: Naemi Csoma / Jonathan M Machin / James M Whitehouse / Raquel Rodrìguez-Alonso / Monika Olejnik / Adam K Cahill / Seung-Hyun Cho / Till F Schäberle / Bogdan I Iorga / Neil A Ranson / Sheena E Radford / Antonio N Calabrese / Jean-François Collet /
Abstract: The β-barrel assembly machinery (BAM) inserts β-barrel proteins into the outer membrane of Gram-negative bacteria, forming an essential permeability barrier. The core BAM component, BamA, is a β- ...The β-barrel assembly machinery (BAM) inserts β-barrel proteins into the outer membrane of Gram-negative bacteria, forming an essential permeability barrier. The core BAM component, BamA, is a β-barrel protein with an N-terminal periplasmic extension comprising five polypeptide transport-associated (POTRA) domains. Whilst BamA's structure is well characterised, it remains unclear how β-barrel and POTRA domain motions are coordinated. Using BamA variants with mutations in the hinge region between these two domains, we demonstrate that hinge flexibility is required for BAM function. Cryo-electron microscopy suggests that hinge rigidity impairs function by structurally decoupling these domains. A screen for spontaneous suppressors identified a mutation at position T434 in an extracellular loop of BamA, which has been previously shown to suppress BAM defects. Studying this variant provides insights into its function as a general rescue mechanism. Our findings underscore how BamA's sequence has been evolutionarily optimised for efficient function.
History
DepositionOct 28, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51930.png

Downloads & links

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Map

FileDownload / File: emd_51930.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli BAM with LVPR insertion in POTRA-barrel domain linker region.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.014709088 - 0.024121856
Average (Standard dev.)0.000099758385 (±0.00078384276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for E. coli BAM with...

Fileemd_51930_half_map_1.map
AnnotationHalf map 1 for E. coli BAM with LVPR insertion in POTRA/barrel domain linker region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for E. coli BAM with...

Fileemd_51930_half_map_2.map
AnnotationHalf map 2 for E. coli BAM with LVPR insertion in POTRA/barrel domain linker region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion

EntireName: BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion
Components
  • Complex: BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion
    • Protein or peptide: Outer membrane protein assembly factor BamA
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamC
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamE

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Supramolecule #1: BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion

SupramoleculeName: BAM (beta-barrel assembly machinery) complex with BamA LVPR insertion
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified as a complex with the insertion
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1
Details: Insertion of LVPR linker in the hinge region (before G410)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 81.203562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV KAVVTPLPRN RVDLKLVFQE GVSAEIQQI NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LDRGYARFNI DSTQVSLTPD K KGIYVTVN ...String:
PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV KAVVTPLPRN RVDLKLVFQE GVSAEIQQI NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LDRGYARFNI DSTQVSLTPD K KGIYVTVN ITEGDQYKLS GVEVSGNLAG HSAEIEQLTK IEPGELYNGT KVTKMEDDIK KLLGRYGYAY PRVQSMPEIN DA DKTVKLR VNVDAGNRFY VRKIRFEGND TSKDAVLRRE MRQMEGAWLG SDLVDQGKER LNRLGFFETV DTDTQRVPGS PDQ VDVVYK VKERNTLVPR GSFNFGIGYG TESGVSFQAG VQQDNWLGTG YAVGINGTKN DYQTYAELSV TNPYFTVDGV SLGG RLFYN DFQADDADLS DYTNKSYGTD VTLGFPINEY NSLRAGLGYV HNSLSNMQPQ VAMWRYLYSM GEHPSTSDQD NSFKT DDFT FNYGWTYNKL DRGYFPTDGS RVNLTGKVTI PGSDNEYYKV TLDTATYVPI DDDHKWVVLG RTRWGYGDGL GGKEMP FYE NFYAGGSSTV RGFQSNTIGP KAVYFPHQAS NYDPDYDYEC ATQDGAKDLC KSDDAVGGNA MAVASLEFIT PTPFISD KY ANSVRTSFFW DMGTVWDTNW DSSQYSGYPD YSDPSNIRMS AGIALQWMSP LGPLVFSYAQ PFKKYDGDKA EQFQFNIG K TW

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 39.692156 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LFNSEEDVVK MSPLPTVENQ FTPTTAWSTS VGSGIGNFYS NLHPALADNV VYAADRAGLV KALNADDGKE IWSVSLAEKD GWFSKEPAL LSGGVTVSGG HVYIGSEKAQ VYALNTSDGT VAWQTKVAGE ALSRPVVSDG LVLIHTSNGQ LQALNEADGA V KWTVNLDM ...String:
LFNSEEDVVK MSPLPTVENQ FTPTTAWSTS VGSGIGNFYS NLHPALADNV VYAADRAGLV KALNADDGKE IWSVSLAEKD GWFSKEPAL LSGGVTVSGG HVYIGSEKAQ VYALNTSDGT VAWQTKVAGE ALSRPVVSDG LVLIHTSNGQ LQALNEADGA V KWTVNLDM PSLSLRGESA PTTAFGAAVV GGDNGRVSAV LMEQGQMIWQ QRISQATGST EIDRLSDVDT TPVVVNGVVF AL AYNGNLT ALDLRSGQIM WKRELGSVND FIVDGNRIYL VDQNDRVMAL TIDGGVTLWT QSDLLHRLLT SPVLYNGNLV VGD SEGYLH WINVEDGRFV AQQKVDSSGF QTEPVAADGK LLIQAKDGTV YSITR

UniProtKB: Outer membrane protein assembly factor BamB

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Macromolecule #3: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.884758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CSSDSRYKRQ VSGDEAYLEA APLAELHAPA GMILPVTSGD YAIPVTNGSG AVGKALDIRP PAQPLAL

UniProtKB: Outer membrane protein assembly factor BamC

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Macromolecule #4: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.008967 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EVPDNPPNEI YATAQQKLQD GNWRQAITQL EALDNRYPFG PYSQQVQLDL IYAYYKNADL PLAQAAIDRF IRLNPTHPNI DYVMYMRGL TNMALDDSAL QGFFGVDRSD RDPQHARAAF SDFSKLVRGY PNSQYTTDAT KRLVFLKDRL AKYEYSVAEY Y TERGAWVA ...String:
EVPDNPPNEI YATAQQKLQD GNWRQAITQL EALDNRYPFG PYSQQVQLDL IYAYYKNADL PLAQAAIDRF IRLNPTHPNI DYVMYMRGL TNMALDDSAL QGFFGVDRSD RDPQHARAAF SDFSKLVRGY PNSQYTTDAT KRLVFLKDRL AKYEYSVAEY Y TERGAWVA VVNRVEGMLR DYPDTQATRD ALPLMENAYR QMQMNAQAEK VAKIIAANSS

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.100229 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
LERVVYRPDI NQGNYLTAND VSKIRVGMTQ QQVAYALGTP LMSDPFGTNT WFYVFRQQPG HEGVTQQTLT LTFNSSGVLT NIDNKPALS GN

UniProtKB: Outer membrane protein assembly factor BamE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Details: 60 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Generated ab initio in in RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127056
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsFitting was done in ISOLDE and the models manually adjusted in coot, coupled with phenix real-space refine minimisation.
Output model

PDB-9h84:
BAM-hinge (LVPR)

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