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- EMDB-51933: BAM-hinge (LVPR) suppressor (T434A) -

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Basic information

Entry
Database: EMDB / ID: EMD-51933
TitleBAM-hinge (LVPR) suppressor (T434A)
Map dataMap for BAM-hinge (LVPR) suppressor, which has an LVPR insert between BamA barrel and POTRA domain and the T434A BamA mutation.
Sample
  • Complex: BAM (beta-barrel assembly machinery) complex with BamA GSGS insertion and T434A BamA mutation
    • 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 / response to antibiotic / 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: 4.0 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_51933.png

Downloads & links

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Map

FileDownload / File: emd_51933.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap for BAM-hinge (LVPR) suppressor, which has an LVPR insert between BamA barrel and POTRA domain and the T434A BamA mutation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 400 pix.
= 364. Å		0.91 Å/pix.
x 400 pix.
= 364. Å		0.91 Å/pix.
x 400 pix.
= 364. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.28293535 - 0.6568976
Average (Standard dev.)0.0016090063 (±0.015584016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 364.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for BAM-hinge (LVPR) suppressor, which...

Fileemd_51933_half_map_1.map
AnnotationHalf map 1 for BAM-hinge (LVPR) suppressor, which has an LVPR insert between BamA barrel and POTRA domain and the T434A BamA mutation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for BAM-hinge (LVPR) suppressor, which...

Fileemd_51933_half_map_2.map
AnnotationHalf map 2 for BAM-hinge (LVPR) suppressor, which has an LVPR insert between BamA barrel and POTRA domain and the T434A BamA mutation.
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 GSGS inser...

EntireName: BAM (beta-barrel assembly machinery) complex with BamA GSGS insertion and T434A BamA mutation
Components
  • Complex: BAM (beta-barrel assembly machinery) complex with BamA GSGS insertion and T434A BamA mutation
    • 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 GSGS inser...

SupramoleculeName: BAM (beta-barrel assembly machinery) complex with BamA GSGS insertion and T434A BamA mutation
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: LVPR insert before residue G410, T434A mutation. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 88.951312 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF QEGVSAEIQQ I NIVGNHAF ...String:
AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF QEGVSAEIQQ I NIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NIDSTQVSLT PDKKGIYVTV NI TEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYPRVQSMPE INDADKTVKL RVN VDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDTDTQRVP GSPDQVDVVY KVKE RNTLV PRGSFNFGIG YGAESGVSFQ AGVQQDNWLG TGYAVGINGT KNDYQTYAEL SVTNPYFTVD GVSLGGRLFY NDFQA DDAD LSDYTNKSYG TDVTLGFPIN EYNSLRAGLG YVHNSLSNMQ PQVAMWRYLY SMGEHPSTSD QDNSFKTDDF TFNYGW TYN KLDRGYFPTD GSRVNLTGKV TIPGSDNEYY KVTLDTATYV PIDDDHKWVV LGRTRWGYGD GLGGKEMPFY ENFYAGG SS TVRGFQSNTI GPKAVYFPHQ ASNYDPDYDY ECATQDGAKD LCKSDDAVGG NAMAVASLEF ITPTPFISDK YANSVRTS F FWDMGTVWDT NWDSSQYSGY PDYSDPSNIR MSAGIALQWM SPLGPLVFSY AQPFKKYDGD KAEQFQFNIG KTW

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: 39.882375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: CSLFNSEEDV VKMSPLPTVE NQFTPTTAWS TSVGSGIGNF YSNLHPALAD NVVYAADRAG LVKALNADDG KEIWSVSLAE KDGWFSKEP ALLSGGVTVS GGHVYIGSEK AQVYALNTSD GTVAWQTKVA GEALSRPVVS DGLVLIHTSN GQLQALNEAD G AVKWTVNL ...String:
CSLFNSEEDV VKMSPLPTVE NQFTPTTAWS TSVGSGIGNF YSNLHPALAD NVVYAADRAG LVKALNADDG KEIWSVSLAE KDGWFSKEP ALLSGGVTVS GGHVYIGSEK AQVYALNTSD GTVAWQTKVA GEALSRPVVS DGLVLIHTSN GQLQALNEAD G AVKWTVNL DMPSLSLRGE SAPTTAFGAA VVGGDNGRVS AVLMEQGQMI WQQRISQATG STEIDRLSDV DTTPVVVNGV VF ALAYNGN LTALDLRSGQ IMWKRELGSV NDFIVDGNRI YLVDQNDRVM ALTIDGGVTL WTQSDLLHRL LTSPVLYNGN LVV GDSEGY LHWINVEDGR FVAQQKVDSS GFQTEPVAAD GKLLIQAKDG TVYSITR

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: 34.40125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: CSSDSRYKRQ VSGDEAYLEA APLAELHAPA GMILPVTSGD YAIPVTNGSG AVGKALDIRP PAQPLALVSG ARTQFTGDTA SLLVENGRG NTLWPQVVSV LQAKNYTITQ RDDAGQTLTT DWVQWNRLDE DEQYRGRYQI SVKPQGYQQA VTVKLLNLEQ A GKPVADAA ...String:
CSSDSRYKRQ VSGDEAYLEA APLAELHAPA GMILPVTSGD YAIPVTNGSG AVGKALDIRP PAQPLALVSG ARTQFTGDTA SLLVENGRG NTLWPQVVSV LQAKNYTITQ RDDAGQTLTT DWVQWNRLDE DEQYRGRYQI SVKPQGYQQA VTVKLLNLEQ A GKPVADAA SMQRYSTEMM NVISAGLDKS ATDAANAAQN RASTTMDVQS AADDTGLPML VVRGPFNVVW QRLPAALEKV GM KVTDSTR SQGNMAVTYK PLSDSDWQEL GASDPGLASG DYKLQVGDLD NRSSLQFIDP KGHTLTQSQN DALVAVFQAA FSK

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: 25.816818 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: CSGSKEEVPD NPPNEIYATA QQKLQDGNWR QAITQLEALD NRYPFGPYSQ QVQLDLIYAY YKNADLPLAQ AAIDRFIRLN PTHPNIDYV MYMRGLTNMA LDDSALQGFF GVDRSDRDPQ HARAAFSDFS KLVRGYPNSQ YTTDATKRLV FLKDRLAKYE Y SVAEYYTE ...String:
CSGSKEEVPD NPPNEIYATA QQKLQDGNWR QAITQLEALD NRYPFGPYSQ QVQLDLIYAY YKNADLPLAQ AAIDRFIRLN PTHPNIDYV MYMRGLTNMA LDDSALQGFF GVDRSDRDPQ HARAAFSDFS KLVRGYPNSQ YTTDATKRLV FLKDRLAKYE Y SVAEYYTE RGAWVAVVNR VEGMLRDYPD TQATRDALPL MENAYRQMQM NAQAEKVAKI IAANSSNT

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: 10.391554 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CSTLERVVYR PDINQGNYLT ANDVSKIRVG MTQQQVAYAL GTPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKP ALSGN

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) / Number grids imaged: 1 / Number real images: 7813 / Average electron dose: 39.8 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 RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Final reconstruction in cryoSPARC, postprocessing and resolution estimation in RELION.
Number images used: 62266
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9h89:
BAM-hinge (LVPR) suppressor (T434A)

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