+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26111 | |||||||||
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Title | BamABCDE bound to substrate EspP in the open-sheet EspP state | |||||||||
Map data | BAM-MBP-76EspP open-sheet EspP state | |||||||||
Sample |
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Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / detection of maltose stimulus / maltose transport complex / protein insertion into membrane / carbohydrate transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / maltose binding / maltose transport / maltodextrin transmembrane transport ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / detection of maltose stimulus / maltose transport complex / protein insertion into membrane / carbohydrate transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / serine-type endopeptidase activity / DNA damage response / cell surface / proteolysis / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Doyle MT / Jimah JR / Dowdy T / Ohlemacher SI / Larion M / Hinshaw JE / Bernstein HD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell / Year: 2022 Title: Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Authors: Matthew Thomas Doyle / John R Jimah / Tyrone Dowdy / Shannon I Ohlemacher / Mioara Larion / Jenny E Hinshaw / Harris D Bernstein / Abstract: Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known ...Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "β signal" motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26111.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-26111-v30.xml emd-26111.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26111_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_26111.png | 52.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26111 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26111 | HTTPS FTP |
-Validation report
Summary document | emd_26111_validation.pdf.gz | 334.8 KB | Display | EMDB validaton report |
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Full document | emd_26111_full_validation.pdf.gz | 334.4 KB | Display | |
Data in XML | emd_26111_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_26111_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26111 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26111 | HTTPS FTP |
-Related structure data
Related structure data | 7tt5MC 7tszC 7tt0C 7tt1C 7tt2C 7tt3C 7tt4C 7tt6C 7tt7C 7ttcC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26111.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | BAM-MBP-76EspP open-sheet EspP state | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07382 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : BamABCDE bound to substrate EspP in the open-sheet EspP state
Entire | Name: BamABCDE bound to substrate EspP in the open-sheet EspP state |
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Components |
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-Supramolecule #1: BamABCDE bound to substrate EspP in the open-sheet EspP state
Supramolecule | Name: BamABCDE bound to substrate EspP in the open-sheet EspP state type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
-Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Serine protease ...
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP chimera type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 83.429984 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK T WEEIPALD ...String: AWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK T WEEIPALD KELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DT DYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDE GLEAVN KDKPLGAVAL KSYEEELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNS GSNIE LVSAPKDTNE NVFKASKQTI GFSDVTPVIT TRETGENLYF QGGDDKITWS LTGYNTVANK EATRNAAALF SVDYK AFLN EVNNLNKRMG DLRDINGEAG AWARIMSGTG SASGGFSDNY THVQVGVDKK HELDGLDLFT GFTVTHTDSS ASADVF SGK TKSVGAGLYA SAMFDSGAYI DLIGKYVHHD NEYTATFAGL GTRDYSTHSW YAGAEAGYRY HVTEDAWIEP QAELVYG SV SGKQFAWKDQ GMHLSMKDKD YNPLIGRTGV DVGKSFSGKD WKVTARAGLG YQFDLLANGE TVLRDASGEK RIKGEKDS R MLMSVGLNAE IRDNVRFGLE FEKSAFGKYN VDNAVNANFR YCF |
-Macromolecule #2: Outer membrane protein assembly factor BamA
Macromolecule | Name: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 89.750094 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AHHHHHHHHG GEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF Q EGVSAEIQ ...String: AHHHHHHHHG GEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF Q EGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NIDSTQVSLT PD KKGIYVT VNITEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYPRVQSMPE IND ADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDTDTQRVP GSPD QVDVV YKVKERNTGC FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTVDGVSL GGRLF YNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSDQDNS FKTDDF TFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDGLGG KEMPFYE NF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFITPT PFISDKYA N SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAEQ FQFNIGKTW |
-Macromolecule #3: Outer membrane protein assembly factor BamE
Macromolecule | Name: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 10.391554 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: CSTLERVVYR PDINQGNYLT ANDVSKIRVG MTQQQVAYAL GTPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKP ALSGN |
-Macromolecule #4: Outer membrane protein assembly factor BamD
Macromolecule | Name: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25.816818 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #5: Outer membrane protein assembly factor BamC
Macromolecule | Name: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 34.40125 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 60.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |