[English] 日本語
Yorodumi
- EMDB-56543: Lid-engaged Complex: BAM bound BepA with lid engaged in membrane -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56543
TitleLid-engaged Complex: BAM bound BepA with lid engaged in membrane
Map data
Sample
  • Complex: BAM BepA
    • 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
KeywordsMetalloprotease / Outer membrane protein / Complex / 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 / protein insertion into membrane / Secretion of toxins / : / 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 / protein insertion into membrane / Secretion of toxins / : / cell outer membrane / metalloendopeptidase activity / outer membrane-bounded periplasmic space / protein-folding chaperone binding / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / zinc ion binding / membrane / metal ion binding / 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 / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 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 / Beta-barrel assembly-enhancing protease / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFenn KL / Ranson NA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)RG.IMCB.128070 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: BAM-BepA complexes in outer membrane protein quality control.
Authors: Katherine L Fenn / Victoria Higgins / Jonathan M Machin / Antonio N Calabrese / Alan Berry / Sheena E Radford / Neil A Ranson /
Abstract: Correct folding of outer membrane proteins (OMPs) by the β-barrel assembly machinery (BAM) is essential for maintaining the outer membrane (OM) barrier function of diderm bacteria. When OMP ...Correct folding of outer membrane proteins (OMPs) by the β-barrel assembly machinery (BAM) is essential for maintaining the outer membrane (OM) barrier function of diderm bacteria. When OMP biogenesis is perturbed, the β-barrel assembly enhancing protease A (BepA) binds to BAM to mediate quality control, but how BepA interacts with BAM and degrades substrate OMPs remains unclear. Here, cryoEM structures of BAM-bound BepA reveals that BepA induces large conformational changes in the BAM complex enabling the enzyme to poise its active site within the periplasmic ring of BAM, beneath the BamA barrel. The lid of BepA is dynamic, embedding two of its water-soluble helices deep into the membrane bilayer when BAM-bound, which readies BepA for proteolysis of misfolding OMPs. Movement of BepA's plug is triggered by OMP binding rather than interaction with BAM, activating the enzyme for cleavage. We reveal BepA preferentially recognises Aromatic-X-Aromatic (Ar-X-Ar) motifs which are enriched in OMP sequences. The results reveal a mechanism for proteolytic degradation by BepA in OMP quality control which requires interaction with BAM, the membrane, and its OMP substrates.
History
DepositionFeb 3, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_56543.png

Downloads & links

-
Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 300 pix.
= 228. Å		0.76 Å/pix.
x 300 pix.
= 228. Å		0.76 Å/pix.
x 300 pix.
= 228. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.5421491 - 0.8807416
Average (Standard dev.)0.003018053 (±0.030485643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_56543_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_56543_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BAM BepA

EntireName: BAM BepA
Components
  • Complex: BAM BepA
    • 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

-
Supramolecule #1: BAM BepA

SupramoleculeName: BAM BepA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: The BAM complex bound to BepA crosslinked in vivo between BamA(P723C) and BepA(L186C)
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 KDa

-
Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 88.520766 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 RNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTVDGVSL GGRLFYNDFQ ADDAD LSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSDQDNS FKTDDFTFNY GWTYNK LDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDGLGG KEMPFYENFY AGGSSTV RG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFITPT CFISDKYANS VRTSFFWD M GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAEQ FQFNIGKTW

UniProtKB: Outer membrane protein assembly factor BamA

-
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

-
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

-
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

-
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: 11.610833 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CSTLERVVYR PDINQGNYLT ANDVSKIRVG MTQQQVAYAL GTPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKP ALSGNGGHHH HHHHH

UniProtKB: Outer membrane protein assembly factor BamE

-
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 (E. coli)
Molecular weightTheoretical: 54.2385 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DSADTLPDMG TSAGSTLSIG QEMQMGDYYV RQLRGSAPLI NDPLLTQYIN SLGMRLVSHA NSVKTPFHFF LINNDEINAF AFFGGNVVL HSALFRYSDN ESQLASVMAH EISHVTQRHL ARAMEDQQRS APLTWVGALG SILLAMASPQ AGMAALTGTC A GTRQGMIS ...String:
DSADTLPDMG TSAGSTLSIG QEMQMGDYYV RQLRGSAPLI NDPLLTQYIN SLGMRLVSHA NSVKTPFHFF LINNDEINAF AFFGGNVVL HSALFRYSDN ESQLASVMAH EISHVTQRHL ARAMEDQQRS APLTWVGALG SILLAMASPQ AGMAALTGTC A GTRQGMIS FTQQNEQEAD RIGIQVLQRS GFDPQAMPTF LEKLLDQARY SSRPPEILLT HPLPESRLAD ARNRANQMRP MV VQSSEDF YLAKARTLGM YNSGRNQLTS DLLDEWAKGN VRQQRAAQYG RALQAMEANK YDEARKTLQP LLAAEPGNAW YLD LATDID LGQNKANEAI NRLKNARDLR TNPVLQLNLA NAYLQGGQPQ EAANILNRYT FNNKDDSNGW DLLAQAEAAL NNRD QELAA RAEGYALAGR LDQAISLLSS ASSQVKLGSL QQARYDARID QLRQLQERFK PYTKMGSSAW SHPQFEKGGG SGGGS GGSA WSHPQFEK

UniProtKB: Beta-barrel assembly-enhancing protease

-
Macromolecule #7: ZINC ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsBuffer: 20mM Tris pH 8, 150mM NaCl, 0.05% DDM

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4200000
CTF correctionSoftware - Name: CTFFIND (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 126000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5ljo

source_name: PDB, initial_model_type: experimental model
chain_id: F, source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-28jl:
Lid-engaged Complex: BAM bound BepA with lid engaged in membrane

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more