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- EMDB-24481: The structure of BAM in complex with EspP at 7 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-24481
TitleThe structure of BAM in complex with EspP at 7 Angstrom resolution
Map data
Sample
  • Complex: Structure of a BAM/EspP hybrid-barrel intermediate
    • Protein or peptide: Maltodextrin-binding protein,Autotransporter outer membrane beta-barrel domain-containing protein chimera
    • 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
  • Ligand: water
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / carbohydrate transmembrane transporter activity / cell outer membrane / periplasmic space / cell adhesion / 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 / SmpA / OmlA family ...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 / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 BamE / Maltodextrin-binding protein / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsWu RR / Noinaj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01GM127884 United States
CitationJournal: Nat Commun / Year: 2021
Title: Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM.
Authors: Runrun Wu / Jeremy W Bakelar / Karl Lundquist / Zijian Zhang / Katie M Kuo / David Ryoo / Yui Tik Pang / Chen Sun / Tommi White / Thomas Klose / Wen Jiang / James C Gumbart / Nicholas Noinaj /
Abstract: In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely ...In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.
History
DepositionJul 20, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rj5
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rj5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24481.png

Downloads & links

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Map

FileDownload / File: emd_24481.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0025 / Movie #1: 0.005
Minimum - Maximum-0.014063502 - 0.027362306
Average (Standard dev.)6.2542385e-05 (±0.0012394626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0140.0270.000

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Supplemental data

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Sample components

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Entire : Structure of a BAM/EspP hybrid-barrel intermediate

EntireName: Structure of a BAM/EspP hybrid-barrel intermediate
Components
  • Complex: Structure of a BAM/EspP hybrid-barrel intermediate
    • Protein or peptide: Maltodextrin-binding protein,Autotransporter outer membrane beta-barrel domain-containing protein chimera
    • 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
  • Ligand: water

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Supramolecule #1: Structure of a BAM/EspP hybrid-barrel intermediate

SupramoleculeName: Structure of a BAM/EspP hybrid-barrel intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 290 MDa

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Macromolecule #1: Maltodextrin-binding protein,Autotransporter outer membrane beta-...

MacromoleculeName: Maltodextrin-binding protein,Autotransporter outer membrane beta-barrel domain-containing protein chimera
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 79.290703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGAKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF T WPLIAADG ...String:
MGAKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF T WPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DT SKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSYEEELVKD PRI AATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVDEALKD AQTGSIELVS APKDTNENVF KASKQTIGFS DVTP VITTR ETDDKITWSL TGYNTVANKE ATRNAAALFS VDYKAFLNEV NNLNKRMGDL RDINGEAGAW ARIMSGTGSA SGGFS DNYT HVQVGVDKKH ELDGLDLFTG FTVTHTDSSA SADVFSGKTK SVGAGLYASA MFDSGAYIDL IGKYVHHDNE YTATFA GLG TRDYSTHSWY AGAEAGYRYH VTEDAWIEPQ AELVYGSVSG KQFAWKDQGM HLSMKDKDYN PLIGRTGVDV GKSFSGK DW KVTARAGLGY QFDLLANGET VLRDASGEKR IKGEKDSRML MSVGLNAEIR DNVRFGLEFE KSAFGKYNVD NAVNANFR Y SF

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Macromolecule #2: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 90.643383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV FQEGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NI DSTQVSL TPDKKGIYVT VNITEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYP RVQSMP EINDADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDT DTQRV PGSPDQVDVV YKVKERNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTV DGVS LGGRLFYNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSD QDN SFKTDDFTFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDG LG GKEMPFYENF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFIT P TPFISDKYAN SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAE QFQFNIGKTW

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Macromolecule #3: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 39.882375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #4: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.530256 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGNGGHHHH HHHH

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ljo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70031
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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