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- EMDB-48253: beta-barrel assembly machine from Escherichia coli in an early st... -

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Basic information

Entry
Database: EMDB / ID: EMD-48253
Titlebeta-barrel assembly machine from Escherichia coli in an early state of substrate assembly
Map databeta-barrel assembly machine from Escherichia coli in an early state of substrate assembly
Sample
  • Complex: BamABCDE bound to BamA substrate in an early folding intermediate state
    • 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: Outer membrane protein assembly factor BamA
  • Protein or peptide: Unknown peptide
Keywordsbeta-barrel assembly machine / outer membrane / folding intermediate / 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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / 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 K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsThomson BD / Kahne D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081059 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI158028 United States
CitationJournal: bioRxiv / Year: 2025
Title: Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism.
Authors: Benjamin D Thomson / Melissa D Marquez / Shaun Rawson / Thiago M A Dos Santos / Stephen C Harrison / Daniel Kahne
Abstract: The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multi-subunit machines. In bacteria, the β-barrel ...The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multi-subunit machines. In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally different substrates into barrels that vary greatly in size. Some larger barrels require globular proteins to plug the barrel lumen. How a single machine can assemble such different barrels is unknown. Here we report three structures representing progressively folded stages of a 16-stranded barrel engaged with BAM, as well as the structure of a late-stage folding intermediate of a 26-stranded substrate folding around its soluble lipoprotein plug on BAM. We find that BAM catalyzes folding of these substrates by a uniform mechanism in which BAM undergoes major distortions to accommodate the nascent barrel.
History
DepositionDec 10, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48253.png

Downloads & links

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Map

FileDownload / File: emd_48253.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbeta-barrel assembly machine from Escherichia coli in an early state of substrate assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.15795383 - 0.2545302
Average (Standard dev.)0.00011170985 (±0.004606031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_48253_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48253_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BamABCDE bound to BamA substrate in an early folding intermediate...

EntireName: BamABCDE bound to BamA substrate in an early folding intermediate state
Components
  • Complex: BamABCDE bound to BamA substrate in an early folding intermediate state
    • 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: Outer membrane protein assembly factor BamA
  • Protein or peptide: Unknown peptide

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Supramolecule #1: BamABCDE bound to BamA substrate in an early folding intermediate...

SupramoleculeName: BamABCDE bound to BamA substrate in an early folding intermediate state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 89.607969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEGHHHHHHH HFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDGD TLLVQVKERP TIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV KAVVTPLPRN RVDLKLVFQE G VSAEIQQI ...String:
AEGHHHHHHH HFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDGD TLLVQVKERP TIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV KAVVTPLPRN RVDLKLVFQE G VSAEIQQI NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LDRGYARFNI DSTQVSLTPD KK GIYVTVN ITEGDQYKLS GVEVSGNLAG HSAEIEQLTK IEPGELYNGT KVTKMEDDIK KLLGRYGYAY PRVQSMPEIN DAD KTVKLR VNVDAGNRFY VRKIRFEGND TSKDAVLRRE MRQMEGAWLG SDLVDQGKER LNRLGFFETV DTDTQRVPGS PDQV DVVYK VKERNTGSFN FGIGYGTESG VSFQAGVQQD NWLGTGYAVG INGTKNDYQT YAELSVTNPY FTVDGVSLGG RLFYN DFQA DDADLSDYTN KSYGTCVTLG FPINEYNSLR AGLGYVHNSL SNMQPQVAMW RYLYSMGEHP STSDQDNSFK TDDFTF NYG WTYNKLDRGY FPTDGSRVNL TGKVTIPGSD NEYYKVTLDT ATYVPIDDDH KWVVLGRTRW GYGDGLGGKE MPFYENF YA GGSSTVRGFQ SNTIGPKAVY FPHQASNYDP DYDYECATQD GAKDLCKSDD AVGGNAMAVA SLEFITPTPF ISDKYANS V RTSFFWDMGT VWDTNWDSSQ YSGYPDYSDP SNIRMSAGIA LQWMSPLGPL VFSYAQPFKK YDGDKAEQFQ FNIGKTW

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 K-12 (bacteria)
Molecular weightTheoretical: 41.918945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 K-12 (bacteria)
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 K-12 (bacteria)
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 K-12 (bacteria)
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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Macromolecule #6: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 62.802703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AWSHPQFEKG GGSGGGSGGS AWSHPQFEKE GFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDG DTLLVQVKER PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV K AVVTPLPR ...String:
AWSHPQFEKG GGSGGGSGGS AWSHPQFEKE GFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDG DTLLVQVKER PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV K AVVTPLPR NRVDLKLVFQ ENTGSFNFGI GYGTESGVSF QAGVQQDNWL GTGYAVGING TKNDYQTYAE LSVTNPYFTV DG VSLGGRL FYNDFQADDA DLSDYTNKSY GTDVTLGFPI NEYNSLRAGL GYVHNSLSNM QPQVAMWRYL YSMGEHPSTS DQD NSFKTD DFTFNYGWTY NKLDRGYFPT DGSRVNLTGK VTIPGSDNEY YKVTLDTATY VPIDDDHKWV VLGRTRWGCG DGLG GKEMP FYENFYAGGS STVRGFQSNT IGPKAVYFPH QASNYDPDYD YECATQDGAK DLCKSDDAVG GNAMAVASLE FITPT PFIS DKYANSVRTS FFWDMGTVWD TNWDSSQYSG YPDYSDPSNI RMSAGIALQW MSPLGPLVFS YAQPFKKYDG DKAEQF QFN IGKTW

UniProtKB: Outer membrane protein assembly factor BamA, Outer membrane protein assembly factor BamA

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Macromolecule #7: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 528.644 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClSodium chloride
0.004 %GDNGlyco-diosgenin
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
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: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20970 / Average exposure time: 1.9 sec. / Average electron dose: 51.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab-initio model generated within cryoSPARC based on the data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 96441
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6v05

source_name: PDB, initial_model_type: experimental model

5ljo

source_name: PDB, initial_model_type: experimental model
Output model

PDB-9mge:
beta-barrel assembly machine from Escherichia coli in an early state of substrate assembly

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