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- EMDB-4061: CryoEM map of E. coli BAM complex (BamABCDE) in DDM micelle -

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Basic information

Entry
Database: EMDB / ID: EMD-4061
TitleCryoEM map of E. coli BAM complex (BamABCDE) in DDM micelle
Map dataE. coli BamABCDE
Sample
  • Complex: BAM complex
    • Protein or peptide: BamA
    • Protein or peptide: BamB
    • Protein or peptide: BamC
    • Protein or peptide: BamD
    • Protein or peptide: BamE
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 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / Outer membrane protein assembly factor BamE domain ...Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / Outer membrane protein assembly factor BamE domain / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Outer membrane protein assembly factor BamB / 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 BamA / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsIadanza MG / Ranson NA / Radford SE / Higgins AJ / Schriffin B / Calabrase AN / Ashcroft AE / Brockwell DJ
CitationJournal: Nat Commun / Year: 2016
Title: Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM.
Authors: Matthew G Iadanza / Anna J Higgins / Bob Schiffrin / Antonio N Calabrese / David J Brockwell / Alison E Ashcroft / Sheena E Radford / Neil A Ranson /
Abstract: The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA-E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins ...The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA-E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a 'lateral gating' motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex and interactions between BamA, B, D and E, and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM.
History
DepositionJul 18, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateJan 18, 2017-
Current statusJan 18, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ljo
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4061.png

Downloads & links

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Map

FileDownload / File: emd_4061.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli BamABCDE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.28031087 - 1.3748333
Average (Standard dev.)0.007866905 (±0.057567354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2801.3750.008

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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: BamA
    • Protein or peptide: BamB
    • Protein or peptide: BamC
    • Protein or peptide: BamD
    • Protein or peptide: BamE

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Supramolecule #1: BAM complex

SupramoleculeName: BAM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pJH114
Molecular weightExperimental: 200 KDa

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Macromolecule #1: BamA

MacromoleculeName: BamA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFAT GNFEDVRVLR DGDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV R VGESLDRT TIADIEKGLE DFYYSVGKYS ASVKAVVTPL PRNRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFAT GNFEDVRVLR DGDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV R VGESLDRT TIADIEKGLE DFYYSVGKYS ASVKAVVTPL PRNRVDLKLV FQEGVSAEIQ QI NIVGNHA FTTDELISHF QLRDEVPWWN VVGDRKYQKQ KLAGDLETLR SYYLDRGYAR FNI DSTQVS LTPDKKGIYV TVNITEGDQY KLSGVEVSGN LAGHSAEIEQ LTKIEPGELY NGTK VTKME DDIKKLLGRY GYAYPRVQSM PEINDADKTV KLRVNVDAGN RFYVRKIRFE GNDTS KDAV LRREMRQMEG AWLGSDLVDQ GKERLNRLGF FETVDTDTQR VPGSPDQVDV VYKVKE RNT GSFNFGIGYG TESGVSFQAG VQQDNWLGTG YAVGINGTKN DYQTYAELSV TNPYFTV DG VSLGGRLFYN DFQADDADLS DYTNKSYGTD VTLGFPINEY NSLRAGLGYV HNSLSNMQ P QVAMWRYLYS MGEHPSTSDQ DNSFKTDDFT FNYGWTYNKL DRGYFPTDGS RVNLTGKVT IPGSDNEYYK VTLDTATYVP IDDDHKWVVL GRTRWGYGDG LGGKEMPFYE NFYAGGSSTV RGFQSNTIG PKAVYFPHQA SNYDPDYDYE CATQDGAKDL CKSDDAVGGN AMAVASLEFI T PTPFISDK YANSVRTSFF WDMGTVWDTN WDSSQYSGYP DYSDPSNIRM SAGIALQWMS PL GPLVFSY AQPFKKYDGD KAEQFQFNIG KTW

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Macromolecule #2: BamB

MacromoleculeName: BamB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALAD NVVYAADRAG LVKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG G HVYIGSEK AQVYALNTSD GTVAWQTKVA GEALSRPVVS DGLVLIHTSN ...String:
MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALAD NVVYAADRAG LVKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG G HVYIGSEK AQVYALNTSD GTVAWQTKVA GEALSRPVVS DGLVLIHTSN GQLQALNEAD GA VKWTVNL DMPSLSLRGE SAPTTAFGAA VVGGDNGRVS AVLMEQGQMI WQQRISQATG STE IDRLSD VDTTPVVVNG VVFALAYNGN LTALDLRSGQ IMWKRELGSV NDFIVDGNRI YLVD QNDRV MALTIDGGVT LWTQSDLLHR LLTSPVLYNG NLVVGDSEGY LHWINVEDGR FVAQQ KVDS SGFQTEPVAA DGKLLIQAKD GTVYSITR

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Macromolecule #3: BamC

MacromoleculeName: BamC / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPV TNGSGAVGKA LDIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ V VSVLQAKN YTITQRDDAG QTLTTDWVQW NRLDEDEQYR GRYQISVKPQ ...String:
MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPV TNGSGAVGKA LDIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ V VSVLQAKN YTITQRDDAG QTLTTDWVQW NRLDEDEQYR GRYQISVKPQ GYQQAVTVKL LN LEQAGKP VADAASMQRY STEMMNVISA GLDKSATDAA NAAQNRASTT MDVQSAADDT GLP MLVVRG PFNVVWQRLP AALEKVGMKV TDSTRSQGNM AVTYKPLSDS DWQELGASDP GLAS GDYKL QVGDLDNRSS LQFIDPKGHT LTQSQNDALV AVFQAAFSK

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Macromolecule #4: BamD

MacromoleculeName: BamD / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQ QVQLDLIYAY YKNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL D DSALQGFF GVDRSDRDPQ HARAAFSDFS KLVRGYPNSQ YTTDATKRLV ...String:
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQ QVQLDLIYAY YKNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL D DSALQGFF GVDRSDRDPQ HARAAFSDFS KLVRGYPNSQ YTTDATKRLV FLKDRLAKYE YS VAEYYTE RGAWVAVVNR VEGMLRDYPD TQATRDALPL MENAYRQMQM NAQAEKVAKI IAA NSSNT

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Macromolecule #5: BamE

MacromoleculeName: BamE / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGN

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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

Concentration6.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH2TRIS
0.05 % (w/v)C24H46O11Dodecyl maltopyranoside
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Pelco EasyGlo
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: Double Blotted: 3ul sample applied, hand blotted then additional 3ul sample applied and blotted and plunge frozen.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 7204 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2
Details: Collected in movie mode at 2 FPS Final data used frames 4-14 for total dose of 20 electrons per square Angstrom
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 48076 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 48076
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

Particle selectionNumber selected: 472857
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)Run from the RELION wrapper
RELION (ver. 1.4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4d0q


Details: Filtered to 90 Angstrom resolution
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 95878
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5ljo:
E. coli BAM complex (BamABCDE) by cryoEM

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