+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40682 | ||||||||||||
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Title | The cryo-EM structure of the EcBAM/EspP(beta1-12) complex | ||||||||||||
Map data | The cryo-EM structure of the EcBAM/EspP(beta1-12) complex | ||||||||||||
Sample |
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Keywords | membrane proteins / protein folding / BAM complex / outer membrane protein / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Hydrolase complex | ||||||||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / membrane / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli 0.1288 (bacteria) / Escherichia coli O157 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Wu R / Noinaj N | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: BAM orchestrates OMP biogenesis using a beta-templating mechanism Authors: Wu R / Ryoo D / Kuo KM / Gumbart JC / Noinaj N | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40682.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-40682-v30.xml emd-40682.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
Images | emd_40682.png | 52.3 KB | ||
Filedesc metadata | emd-40682.cif.gz | 6.7 KB | ||
Others | emd_40682_half_map_1.map.gz emd_40682_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40682 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40682 | HTTPS FTP |
-Related structure data
Related structure data | 8sprMC 8sqaC 8sqbC M: atomic model generated by this map C: citing same article (ref.) |
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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_40682.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The cryo-EM structure of the EcBAM/EspP(beta1-12) complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_40682_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_40682_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BAM/EspP(beta1-12)
Entire | Name: BAM/EspP(beta1-12) |
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Components |
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-Supramolecule #1: BAM/EspP(beta1-12)
Supramolecule | Name: BAM/EspP(beta1-12) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Outer membrane protein assembly factor BamA
Macromolecule | Name: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 88.247477 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 NCGKTW UniProtKB: Outer membrane protein assembly factor BamA |
-Macromolecule #2: Outer membrane protein assembly factor BamB
Macromolecule | Name: Outer membrane protein assembly factor BamB / 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: 39.77923 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDGK EIWSVSLAEK DGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD GLVLIHTSNG QLQALNEADG A VKWTVNLD ...String: SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDGK EIWSVSLAEK DGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD GLVLIHTSNG QLQALNEADG A VKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TEIDRLSDVD TTPVVVNGVV FA LAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQSDLLHRLL TSPVLYNGNL VVG DSEGYL HWINVEDGRF VAQQKVDSSG FQTEPVAADG KLLIQAKDGT VYSITR UniProtKB: Outer membrane protein assembly factor BamB |
-Macromolecule #3: Outer membrane protein assembly factor BamC
Macromolecule | Name: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli 0.1288 (bacteria) |
Molecular weight | Theoretical: 34.298109 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SSDSRYKRQV SGDEAYLEAA PLAELHAPAG MILPVTSGDY AIPVTNGSGA VGKALDIRPP AQPLALVSGA RTQFTGDTAS LLVENGRGN TLWPQVVSVL QAKNYTITQR DDAGQTLTTD WVQWNRLDED EQYRGRYQIS VKPQGYQQAV TVKLLNLEQA G KPVADAAS ...String: SSDSRYKRQV SGDEAYLEAA PLAELHAPAG MILPVTSGDY AIPVTNGSGA VGKALDIRPP AQPLALVSGA RTQFTGDTAS LLVENGRGN TLWPQVVSVL QAKNYTITQR DDAGQTLTTD WVQWNRLDED EQYRGRYQIS VKPQGYQQAV TVKLLNLEQA G KPVADAAS MQRYSTEMMN VISAGLDKSA TDAANAAQNR ASTTMDVQSA ADDTGLPMLV VRGPFNVVWQ RLPAALEKVG MK VTDSTRS QGNMAVTYKP LSDSDWQELG ASDPGLASGD YKLQVGDLDN RSSLQFIDPK GHTLTQSQND ALVAVFQAAF SK UniProtKB: Outer membrane protein assembly factor BamC |
-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: 25.713676 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQA AIDRFIRLNP THPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY TTDATKRLVF LKDRLAKYEY S VAEYYTER ...String: SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQA AIDRFIRLNP THPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY TTDATKRLVF LKDRLAKYEY S VAEYYTER GAWVAVVNRV EGMLRDYPDT QATRDALPLM ENAYRQMQMN AQAEKVAKII AANSSNT UniProtKB: Outer membrane protein assembly factor BamD |
-Macromolecule #5: Outer membrane protein assembly factor BamE
Macromolecule | Name: Outer membrane protein assembly factor BamE / 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: 10.540661 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQT LTLTFNSSGV LTNIDNKPA LSGNGGH UniProtKB: Outer membrane protein assembly factor BamE |
-Macromolecule #6: Serine protease EspP
Macromolecule | Name: Serine protease EspP / type: protein_or_peptide / ID: 6 / 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 O157 (bacteria) |
Molecular weight | Theoretical: 38.77384 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GSIELVSAPK DTNENVFKAS KQTIGFSDVT PVITTRETDD KITWSLTGYN TVANKEATRN AAALFSVDYK AFLNEVSNLN KRMGDLRDI NGEAGCWARI MSGTGSASGG FSDNYTHVQV GVDKKHELDG LDLFTGFTVT HTDSSASADV FSGKTKSVGA G LYASAMFD ...String: GSIELVSAPK DTNENVFKAS KQTIGFSDVT PVITTRETDD KITWSLTGYN TVANKEATRN AAALFSVDYK AFLNEVSNLN KRMGDLRDI NGEAGCWARI MSGTGSASGG FSDNYTHVQV GVDKKHELDG LDLFTGFTVT HTDSSASADV FSGKTKSVGA G LYASAMFD SGAYIDLIGK YVHHDNEYTA TFAGLGTRDY STHSWYAGAE AGYRYHVTED AWIEPQAELV YGSVSGKQFA WK DQGMHLS MKDKDYNPLI GRTGVDVGKS FSGKDWKVTA RAGLGYQFDL LANGETVLRD ASGEKRIKGE KDSRMLMSVG LNA EIRDNV RFGLEFEKSA FGKYNVDNAV NANFRYSF UniProtKB: Serine protease EspP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.47 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145290 |