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Yorodumi- EMDB-33765: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33765 | |||||||||
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Title | BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc | |||||||||
Map data | BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc | |||||||||
Sample |
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Keywords | BAM / BamABCDE / EspP / Gram-negative bacteria / outer membrane protein / outer membrane barrel / BamA / BamB / BamC / BamD / BamE / MEMBRANE PROTEIN | |||||||||
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 / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / response to antibiotic / serine-type endopeptidase activity ...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 / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / response to antibiotic / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli O157:H7 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Shen C / Chang S / Luo Q / Zhang Z / Luo B / Lu G / Zhu X / Wei X / Dong C / Zhang X ...Shen C / Chang S / Luo Q / Zhang Z / Luo B / Lu G / Zhu X / Wei X / Dong C / Zhang X / Tang X / Dong H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang ...Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang / Xiaodi Tang / Haohao Dong / Abstract: The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of ...The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials. All known OMPs share the antiparallel β-strand topology, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33765.map.gz | 49.2 MB | EMDB map data format | |
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Header (meta data) | emd-33765-v30.xml emd-33765.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
Images | emd_33765.png | 61.6 KB | ||
Others | emd_33765_half_map_1.map.gz emd_33765_half_map_2.map.gz | 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33765 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33765 | HTTPS FTP |
-Related structure data
Related structure data | 7ye6MC 7ye4C 8bnzC 8bo2C 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_33765.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc half2
File | emd_33765_half_map_1.map | ||||||||||||
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Annotation | BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc half1
File | emd_33765_half_map_2.map | ||||||||||||
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Annotation | BAM-EspP-pair2 BamA N427C EspP R1297C in nanodisc half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations ...
Entire | Name: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc |
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Components |
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-Supramolecule #1: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations ...
Supramolecule | Name: BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: BAM
Supramolecule | Name: BAM / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Supramolecule #3: EspP
Supramolecule | Name: EspP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6 |
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Source (natural) | Organism: Escherichia coli O157:H7 (bacteria) |
-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 K-12 (bacteria) |
Molecular weight | Theoretical: 90.632422 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: 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 FCFGIGYGTE 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 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 K-12 (bacteria) |
Molecular weight | Theoretical: 41.918945 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN ...String: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN GQLQALNEAD GAVKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TE IDRLSDV DTTPVVVNGV VFALAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQS DLLHRL LTSPVLYNGN LVVGDSEGYL 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 K-12 (bacteria) |
Molecular weight | Theoretical: 36.875277 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: 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 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 K-12 (bacteria) |
Molecular weight | Theoretical: 27.85835 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: 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 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 K-12 (bacteria) |
Molecular weight | Theoretical: 13.530256 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGNGGHHHH HHHH 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:H7 (bacteria) |
Molecular weight | Theoretical: 38.684719 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: NIELVSAPKD TNENVFKASK QTIGFSDVTP VITTRETDDK ITWSLTGYNT VANKEATRNA AALFSVDYKA FLNEVNNLNK RMGDLRDIN GEAGAWARIM SGTGSASGGF SDNYTHVQVG VDKKHELDGL DLFTGFTVTH TDSSASADVF SGKTKSVGAG L YASAMFDS ...String: NIELVSAPKD TNENVFKASK QTIGFSDVTP VITTRETDDK ITWSLTGYNT VANKEATRNA AALFSVDYKA FLNEVNNLNK RMGDLRDIN GEAGAWARIM SGTGSASGGF SDNYTHVQVG VDKKHELDGL DLFTGFTVTH TDSSASADVF SGKTKSVGAG L YASAMFDS GAYIDLIGKY VHHDNEYTAT FAGLGTRDYS THSWYAGAEA GYRYHVTEDA WIEPQAELVY GSVSGKQFAW KD QGMHLSM KDKDYNPLIG RTGVDVGKSF SGKDWKVTAR AGLGYQFDLL ANGETVLRDA SGEKRIKGEK DSRMLMSVGL NAE IRDNVR FGLEFEKSAF GKYNVDNAVN ANFCYSF 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: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl |
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Vitrification | Cryogen name: ETHANE |
Details | BAM-EspP complex structure with BamA-N427C/EspP-R1297C mutations in nanodisc |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 7.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 3723668 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: 7yd5 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198471 |