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- EMDB-55064: BepA-BamABCDE-Nb32 complex in inward open conformation with later... -

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Basic information

Entry
Database: EMDB / ID: EMD-55064
TitleBepA-BamABCDE-Nb32 complex in inward open conformation with lateral seam closed
Map data
Sample
  • Complex: BepA-BamABCDE complex with nanobody32
    • 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
    • Protein or peptide: Beta-barrel assembly-enhancing protease
  • Ligand: ZINC ION
KeywordsM48 metalloprotease family / outer membrane protein / beta-barrel assembly machinery / cell envelope / BepA / BAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / Secretion of toxins / protein insertion into membrane / : / cell outer membrane / metalloendopeptidase activity / outer membrane-bounded periplasmic space ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / Secretion of toxins / protein insertion into membrane / : / cell outer membrane / metalloendopeptidase activity / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / response to antibiotic / cell surface / metal ion binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Beta-barrel assembly-enhancing protease / : / Peptidase M48 / Peptidase family M48 / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamE ...Beta-barrel assembly-enhancing protease / : / Peptidase M48 / Peptidase family M48 / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / 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 / Outer membrane protein assembly factor BamB / BamE-like / Tetratricopeptide repeat / 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 BamA / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Beta-barrel assembly-enhancing protease / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsNguyen VS / Remaut H / Nguyen PC / Voedts H / Collet JF
Funding support Belgium, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G0G0818N Belgium
Research Foundation - Flanders (FWO)12ZM421N Belgium
CitationJournal: Nat Commun / Year: 2026
Title: Stress-induced membrane insertion at the beta-barrel assembly machinery complex regulates BepA metalloprotease activity
Authors: Voedts H / Nguyen PC / Nguyen VS / Leverrier P / Iorga BI / Cho SH / Remaut H / Collet JF
History
DepositionSep 16, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55064.png

Downloads & links

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Map

FileDownload / File: emd_55064.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.52 Å/pix.
x 180 pix.
= 273.6 Å		1.52 Å/pix.
x 180 pix.
= 273.6 Å		1.52 Å/pix.
x 180 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.16291063 - 9.723027999999999
Average (Standard dev.)0.027699241 (±0.40493459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55064_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55064_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BepA-BamABCDE complex with nanobody32

EntireName: BepA-BamABCDE complex with nanobody32
Components
  • Complex: BepA-BamABCDE complex with nanobody32
    • 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
    • Protein or peptide: Beta-barrel assembly-enhancing protease
  • Ligand: ZINC ION

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Supramolecule #1: BepA-BamABCDE complex with nanobody32

SupramoleculeName: BepA-BamABCDE complex with nanobody32 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: The complex was purified from over-expression of a BepA inactive mutant in E. coli K12. BepA has a twinstrep tag at the C-terminal. The complex was first pulled on twinstrep tag using Strep- ...Details: The complex was purified from over-expression of a BepA inactive mutant in E. coli K12. BepA has a twinstrep tag at the C-terminal. The complex was first pulled on twinstrep tag using Strep-TactinXT 4Flow high capacity resin, then mixed with BamA nanobody32-his and pulled on his tag using Ni-NTA resin.
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 260 KDa

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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: native protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 90.643383 KDa
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV FQEGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NI DSTQVSL TPDKKGIYVT VNITEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYP RVQSMP EINDADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDT DTQRV PGSPDQVDVV YKVKERNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTV DGVS LGGRLFYNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSD QDN SFKTDDFTFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDG LG GKEMPFYENF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFIT P TPFISDKYAN SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAE QFQFNIGKTW

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 BW25113 (bacteria)
Molecular weightTheoretical: 41.918945 KDa
SequenceString: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN ...String:
MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN GQLQALNEAD GAVKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TE IDRLSDV DTTPVVVNGV VFALAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQS DLLHRL LTSPVLYNGN LVVGDSEGYL HWINVEDGRF VAQQKVDSSG FQTEPVAADG KLLIQAKDGT VYSITR

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 BW25113 (bacteria)
Molecular weightTheoretical: 36.875277 KDa
SequenceString: MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ ...String:
MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ GYQQAVTVKL LNLEQAGKPV ADAASMQRYS TEMMNVISAG LDKSATDAAN AAQNRASTTM DVQSAADDTG LP MLVVRGP FNVVWQRLPA ALEKVGMKVT DSTRSQGNMA VTYKPLSDSD WQELGASDPG LASGDYKLQV GDLDNRSSLQ FID PKGHTL TQSQNDALVA VFQAAFSK

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 BW25113 (bacteria)
Molecular weightTheoretical: 27.85835 KDa
SequenceString: MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV ...String:
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV FLKDRLAKYE YSVAEYYTER GAWVAVVNRV EGMLRDYPDT QATRDALPLM ENAYRQMQMN AQAEKVAKII AA NSSNT

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 BW25113 (bacteria)
Molecular weightTheoretical: 12.310977 KDa
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGN

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: Beta-barrel assembly-enhancing protease

MacromoleculeName: Beta-barrel assembly-enhancing protease / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 53.962766 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MFRQLKKNLV ATLIAAMTIG QVAPAFADSA DTLPDMGTSA GSTLSIGQEM QMGDYYVRQL RGSAPLINDP LLTQYINSLG MRLVSHANS VKTPFHFFLI NNDEINAFAF FGGNVVLHSA LFRYSDNESQ LASVMAHEIS HVTQRHLARA MEDQQRSAPL T WVGALGSI ...String:
MFRQLKKNLV ATLIAAMTIG QVAPAFADSA DTLPDMGTSA GSTLSIGQEM QMGDYYVRQL RGSAPLINDP LLTQYINSLG MRLVSHANS VKTPFHFFLI NNDEINAFAF FGGNVVLHSA LFRYSDNESQ LASVMAHEIS HVTQRHLARA MEDQQRSAPL T WVGALGSI LLAMASPQAG MAALTGTLAG TRQGMISFTQ QNEQEADRIG IQVLQRSGFD PQAMPTFLEK LLDQARYSSR PP EILLTHP LPESRLADAR NRANQMRPMV VQSSEDFYLA KARTLGMYNS GRNQLTSDLL DEWAKGNVRQ QRAAQYGRAL QAM EANKYD EARKTLQPLL AAEPGNAWYL DLATDIDLGQ NKANEAINRL KNARDLRTNP VLQLNLANAY LQGGQPQEAA NILN RYTFN NKDDSNGWDL LAQAEAALNN RDQELAARAE GYALAGRLDQ AISLLSSASS QVKLGSLQQA RYDARIDQLR QLQER FKPY TKM

UniProtKB: Beta-barrel assembly-enhancing protease

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3trisaminomethane
150.0 mMNaClSodium Chloride
300.0 mMC3H2N4Imidazole
0.03 %C24H46O11n-dodecyl-beta-D-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3 / Details: 2-side blotting for 5 seconds.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10904 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3449013
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9hg5

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24620
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 38730
FSC plot (resolution estimation)

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