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- EMDB-10250: BamABCDE in MSP1D1 nanodisc ensemble 0-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-10250
TitleBamABCDE in MSP1D1 nanodisc ensemble 0-3
Map dataBamABCDE in MSP1D1 nanodisc ensemble 0-3
Sample
  • Complex: Bam complex
    • 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 / OMP / beta-barrel / folding / insertion / 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
Similarity search - Function
Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat ...Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / : / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesescherichia coli (E. coli) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsIadanza MG / Ranson NA
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P018491/1 United Kingdom
Wellcome Trust090932/Z/09/Z United Kingdom
Wellcome Trust094232/Z/10/Z United Kingdom
Wellcome Trust105220/Z/14/Z United Kingdom
CitationJournal: Commun Biol / Year: 2020
Title: Distortion of the bilayer and dynamics of the BAM complex in lipid nanodiscs.
Authors: Matthew G Iadanza / Bob Schiffrin / Paul White / Matthew A Watson / Jim E Horne / Anna J Higgins / Antonio N Calabrese / David J Brockwell / Roman Tuma / Antreas C Kalli / Sheena E Radford / Neil A Ranson /
Abstract: The β-barrel assembly machinery (BAM) catalyses the folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria by mechanisms that remain ...The β-barrel assembly machinery (BAM) catalyses the folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria by mechanisms that remain unclear. Here, we present an ensemble of cryoEM structures of the E. coli BamABCDE (BAM) complex in lipid nanodiscs, determined using multi-body refinement techniques. These structures, supported by single-molecule FRET measurements, describe a range of motions in the BAM complex, mostly localised within the periplasmic region of the major subunit BamA. The β-barrel domain of BamA is in a 'lateral open' conformation in all of the determined structures, suggesting that this is the most energetically favourable species in this bilayer. Strikingly, the BAM-containing lipid nanodisc is deformed, especially around BAM's lateral gate. This distortion is also captured in molecular dynamics simulations, and provides direct structural evidence for the lipid 'disruptase' activity of BAM, suggested to be an important part of its functional mechanism.
History
DepositionAug 23, 2019-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0127
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sn3
  • Surface level: 0.0127
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10250.png

Downloads & links

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Map

FileDownload / File: emd_10250.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBamABCDE in MSP1D1 nanodisc ensemble 0-3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0127 / Movie #1: 0.0127
Minimum - Maximum-0.010802871 - 0.035858717
Average (Standard dev.)0.00018429238 (±0.0016876005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.500319.500319.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0110.0360.000

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Supplemental data

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Sample components

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Entire : Bam complex

EntireName: Bam complex
Components
  • Complex: Bam complex
    • 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 complex

SupramoleculeName: Bam complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In MSP1D1 nanodisc with E. coli polar lipid extract
Source (natural)Organism: escherichia coli (E. coli)
Molecular weightTheoretical: 200 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 87.783945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FVVKDIHFEG LQRVAVGAAL LSMPVRTGDT VNDEDISNTI RALFATGNFE DVRVLRDGDT LLVQVKERPT IASITFSGNK SVKDDMLKQ NLEASGVRVG ESLDRTTIAD IEKGLEDFYY SVGKYSASVK AVVTPLPRNR VDLKLVFQEG VSAEIQQINI V GNHAFTTD ...String:
FVVKDIHFEG LQRVAVGAAL LSMPVRTGDT VNDEDISNTI RALFATGNFE DVRVLRDGDT LLVQVKERPT IASITFSGNK SVKDDMLKQ NLEASGVRVG ESLDRTTIAD IEKGLEDFYY SVGKYSASVK AVVTPLPRNR VDLKLVFQEG VSAEIQQINI V GNHAFTTD ELISHFQLRD EVPWWNVVGD RKYQKQKLAG DLETLRSYYL DRGYARFNID STQVSLTPDK KGIYVTVNIT EG DQYKLSG VEVSGNLAGH SAEIEQLTKI EPGELYNGTK VTKMEDDIKK LLGRYGYAYP RVQSMPEIND ADKTVKLRVN VDA GNRFYV RKIRFEGNDT SKDAVLRREM RQMEGAWLGS DLVDQGKERL NRLGFFETVD TDTQRVPGSP DQVDVVYKVK ERNT GSFNF GIGYGTESGV SFQAGVQQDN WLGTGYAVGI NGTKNDYQTY AELSVTNPYF TVDGVSLGGR LFYNDFQADD ADLSD YTNK SYGTDVTLGF PINEYNSLRA GLGYVHNSLS NMQPQVAMWR YLYSMGEHPS TSDQDNSFKT DDFTFNYGWT YNKLDR GYF PTDGSRVNLT GKVTIPGSDN EYYKVTLDTA TYVPIDDDHK WVVLGRTRWG YGDGLGGKEM PFYENFYAGG SSTVRGF QS NTIGPKAVYF PHQASNYDPD YDYECATQDG AKDLCKSDDA VGGNAMAVAS LEFITPTPFI SDKYANSVRT SFFWDMGT V WDTNWDSSQY SGYPDYSDPS NIRMSAGIAL QWMSPLGPLV FSYAQPFKKY DGDKAEQFQF NI

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: 39.692156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LFNSEEDVVK MSPLPTVENQ FTPTTAWSTS VGSGIGNFYS NLHPALADNV VYAADRAGLV KALNADDGKE IWSVSLAEKD GWFSKEPAL LSGGVTVSGG HVYIGSEKAQ VYALNTSDGT VAWQTKVAGE ALSRPVVSDG LVLIHTSNGQ LQALNEADGA V KWTVNLDM ...String:
LFNSEEDVVK MSPLPTVENQ FTPTTAWSTS VGSGIGNFYS NLHPALADNV VYAADRAGLV KALNADDGKE IWSVSLAEKD GWFSKEPAL LSGGVTVSGG HVYIGSEKAQ VYALNTSDGT VAWQTKVAGE ALSRPVVSDG LVLIHTSNGQ LQALNEADGA V KWTVNLDM PSLSLRGESA PTTAFGAAVV GGDNGRVSAV LMEQGQMIWQ QRISQATGST EIDRLSDVDT TPVVVNGVVF AL AYNGNLT ALDLRSGQIM WKRELGSVND FIVDGNRIYL VDQNDRVMAL TIDGGVTLWT QSDLLHRLLT SPVLYNGNLV VGD SEGYLH WINVEDGRFV AQQKVDSSGF QTEPVAADGK LLIQAKDGTV YSITR

UniProtKB: UNIPROTKB: A0A2S5ZNM3

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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: 6.096815 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CSSDSRYKRQ VSGDEAYLEA APLAELHAPA GMILPVTSGD YAIPVTNGSG AVGKALDIR

UniProtKB: UNIPROTKB: A0A4T5IPK3

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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: 25.008967 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVPDNPPNEI YATAQQKLQD GNWRQAITQL EALDNRYPFG PYSQQVQLDL IYAYYKNADL PLAQAAIDRF IRLNPTHPNI DYVMYMRGL TNMALDDSAL QGFFGVDRSD RDPQHARAAF SDFSKLVRGY PNSQYTTDAT KRLVFLKDRL AKYEYSVAEY Y TERGAWVA ...String:
EVPDNPPNEI YATAQQKLQD GNWRQAITQL EALDNRYPFG PYSQQVQLDL IYAYYKNADL PLAQAAIDRF IRLNPTHPNI DYVMYMRGL TNMALDDSAL QGFFGVDRSD RDPQHARAAF SDFSKLVRGY PNSQYTTDAT KRLVFLKDRL AKYEYSVAEY Y TERGAWVA VVNRVEGMLR DYPDTQATRD ALPLMENAYR QMQMNAQAEK VAKIIAANSS

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: 9.728837 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ERVVYRPDIN QGNYLTANDV SKIRVGMTQQ QVAYALGTPL MSDPFGTNTW FYVFRQQPGH EGVTQQTLTL TFNSSGVLTN IDNKPAL

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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 15504 / Average exposure time: 10.0 sec. / Average electron dose: 40.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4061


Details: filtered to 60 Angstrom
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 37910
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ljo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6sn3:
BamABCDE in MSP1D1 nanodisc ensemble 0-3

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