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- EMDB-71134: beta-barrel assembly machine from Escherichia coli in an late sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-71134
Titlebeta-barrel assembly machine from Escherichia coli in an late state of LptD assembly
Map dataCombined LptD Bam map
Sample
  • Complex: Late intermediate state of folding of LptD on the beta-barrel assembly machine
    • 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: LPS-assembly lipoprotein LptE
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamA
Keywordsbeta-barrel assembly machine / outer membrane / folding intermediate / MEMBRANE PROTEIN
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / cell outer membrane / lipopolysaccharide binding / protein-macromolecule adaptor activity / cell adhesion ...transporter complex / lipopolysaccharide transport / Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / cell outer membrane / lipopolysaccharide binding / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / membrane / identical protein binding
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC ...LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / 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 / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsThomson BD / Marquez MD / 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: Thomson BD / Marquez MD / Rawson S / dos Santos TMA / Harrison SC / Kahne D
History
DepositionJun 10, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71134.png

Downloads & links

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Map

FileDownload / File: emd_71134.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined LptD Bam map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.74 Å/pix.
x 440 pix.
= 323.84 Å		0.74 Å/pix.
x 440 pix.
= 323.84 Å		0.74 Å/pix.
x 440 pix.
= 323.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.1
Minimum - Maximum-19.042542000000001 - 34.349449999999997
Average (Standard dev.)0.0020356202 (±1.0208341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 323.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Late intermediate state of folding of LptD on the beta-barrel ass...

EntireName: Late intermediate state of folding of LptD on the beta-barrel assembly machine
Components
  • Complex: Late intermediate state of folding of LptD on the beta-barrel assembly machine
    • 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: LPS-assembly lipoprotein LptE
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: Outer membrane protein assembly factor BamB
    • Protein or peptide: Outer membrane protein assembly factor BamA

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Supramolecule #1: Late intermediate state of folding of LptD on the beta-barrel ass...

SupramoleculeName: Late intermediate state of folding of LptD on the beta-barrel assembly machine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.875277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #2: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.85835 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #3: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.310977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #4: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 21.381527 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR ...String:
MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR SDEEQTSTTT DTPATPARVS TTLGN

UniProtKB: LPS-assembly lipoprotein LptE

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Macromolecule #5: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 93.063148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRIPTLLA TMIATALYSQ QGLAADLAWS HPQFEKGGGS GGGSGGSAWS HPQFEKGSGS GGSASQCMLG VPSYDRPLVQ GDTNDLPVT INADHAKGDY PDDAVFTGSV DIMQGNSRLQ ADEVQLHQKE APGQPEPVRT VDALGNVHYD DNQVILKGPK G WANLNTKD ...String:
MKKRIPTLLA TMIATALYSQ QGLAADLAWS HPQFEKGGGS GGGSGGSAWS HPQFEKGSGS GGSASQCMLG VPSYDRPLVQ GDTNDLPVT INADHAKGDY PDDAVFTGSV DIMQGNSRLQ ADEVQLHQKE APGQPEPVRT VDALGNVHYD DNQVILKGPK G WANLNTKD TNVWEGDYQM VGRQGRGKAD LMKQRGENRY TILDNGSFTS CLPGSDTWSV VGSEIIHDRE EQVAEIWNAR FK VGPVPIF YSPYLQLPVG DKRRSGFLIP NAKYTTTNYF EFYLPYYWNI APNMDATCTP HYMHRRGNIM WENEFRYLSQ AGA GLMELD YLPSDKVYED EHPNDDSSRR WLFYWNHSGV MDQVWRFNVY TKVSDPSYFN DFDNKYGSST DGYATQKFSV GYAV QNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ NDVGPFDTRI YGQAVHFVNT RDDMPEATRV HLEPTINLPL SNNWG SINT EAKLLATHYQ QTNLDWYNSR NTTKLDESVN RVMPQFKVDG KMVFERDMEM LAPGYTQTLE PRAQYLYVPY RDQSDI YNY DSSLLQSDYS GLFRDRTYGG LDRIASANQV TTGVTSRIYD DAAVERFNIS VGQIYYFTES RTGDDNITWE NDDKTGS LV WAGDTYWRIS ERWGLRGGIQ YDTRLDNVAT SNSSIEYRRD EDRLVQLNYR YASPEYIQAT LPKYYSTAEQ YKNGISQV G AVASWPIADR WSIVGAYYYD TNANKQADSM LGVQYSSCCY AIRVGYERKL NGWDNDKQHA VYDNAIGFNI ELRGLSSNY GLGTQEMLRS NILPYQNTL

UniProtKB: LPS-assembly protein LptD

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Macromolecule #6: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.918945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #7: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 91.736602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGHHHHHHH HFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDG DTLLVQVKER PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV K AVVTPLPR ...String:
MAMKKLLIAS LLFSSATVYG AEGHHHHHHH HFVVKDIHFE GLQRVAVGAA LLSMPVRTGD TVNDEDISNT IRALFATGNF EDVRVLRDG DTLLVQVKER PTIASITFSG NKSVKDDMLK QNLEASGVRV GESLDRTTIA DIEKGLEDFY YSVGKYSASV K AVVTPLPR NRVDLKLVFQ EGVSAEIQQI NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LD RGYARFN IDSTQVSLTP DKKGIYVTVN ITEGDQYKLS GVEVSGNLAG HSAEIEQLTK IEPGELYNGT KVTKMEDDIK KLL GRYGYA YPRVQSMPEI NDADKTVKLR VNVDAGNRFY VRKIRFEGND TSKDAVLRRE MRQMEGAWLG SDLVDQGKER LNRL GFFET VDTDTQRVPG SPDQVDVVYK VKERNTGSFN FGIGYGTESG VSFQAGVQQD NWLGTGYAVG INGTKNDYQT YAELS VTNP YFTVDGVSLG GRLFYNDFQA DDADLSDYTN KSYGTCVTLG FPINEYNSLR AGLGYVHNSL SNMQPQVAMW RYLYSM GEH PSTSDQDNSF KTDDFTFNYG WTYNKLDRGY FPTDGSRVNL TGKVTIPGSD NEYYKVTLDT ATYVPIDDDH KWVVLGR TR WGYGDGLGGK EMPFYENFYA GGSSTVRGFQ SNTIGPKAVY FPHQASNYDP DYDYECATQD GAKDLCKSDD AVGGNAMA V ASLEFITPTP FISDKYANSV RTSFFWDMGT VWDTNWDSSQ YSGYPDYSDP SNIRMSAGIA LQWMSPLGPL VFSYAQPFK KYDGDKAEQF QFNIGKTW

UniProtKB: Outer membrane protein assembly factor BamA

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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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: TFS FALCON 4i (4k x 4k) / Average electron dose: 49.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
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: OTHER
Details: Ab-initio model generated within cryoSPARC based on the data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79819
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

5lj0

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9p1u:
beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly

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