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- EMDB-40700: The cryo-EM structure of the EcBAM/EspP(beta8-12) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-40700
TitleThe cryo-EM structure of the EcBAM/EspP(beta8-12) complex
Map dataThe cryo-EM structure of the EcBAM/EspP(beta8-12) complex
Sample
  • Complex: BAM/EspP(beta1-12)
    • 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
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Autotransporter protein EspP translocator
Keywordsmembrane proteins / protein folding / BAM complex / outer membrane protein / MEMBRANE PROTEIN
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 / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / serine-type endopeptidase activity / cell surface ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / carbohydrate transmembrane transporter activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / membrane / identical protein binding
Similarity search - Function
Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily ...Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / 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 / Autotransporter, pectate lyase C-like domain superfamily / 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 / Pectin lyase fold/virulence factor / 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 / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamA / Maltose/maltodextrin-binding periplasmic protein / Outer membrane protein assembly factor BamB / Serine protease EspP
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli O157 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWu R / Noinaj N
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123169 United States
CitationJournal: 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
DepositionMay 4, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40700.png

Downloads & links

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Map

FileDownload / File: emd_40700.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM structure of the EcBAM/EspP(beta8-12) complex
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.8756262 - 1.669016
Average (Standard dev.)0.0051739067 (±0.057480957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_40700_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40700_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BAM/EspP(beta1-12)

EntireName: BAM/EspP(beta1-12)
Components
  • Complex: BAM/EspP(beta1-12)
    • 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
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Autotransporter protein EspP translocator

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Supramolecule #1: BAM/EspP(beta1-12)

SupramoleculeName: BAM/EspP(beta1-12) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 88.100305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VVKDIHFEGL QRVAVGAALL SMPVRTGDTV NDEDISNTIR ALFATGNFED VRVLRDGDTL LVQVKERPTI ASITFSGNKS VKDDMLKQN LEASGVRVGE SLDRTTIADI EKGLEDFYYS VGKYSASVKA VVTPLPRNRV DLKLVFQEGV SAEIQQINIV G NHAFTTDE ...String:
VVKDIHFEGL QRVAVGAALL SMPVRTGDTV NDEDISNTIR ALFATGNFED VRVLRDGDTL LVQVKERPTI ASITFSGNKS VKDDMLKQN LEASGVRVGE SLDRTTIADI EKGLEDFYYS VGKYSASVKA VVTPLPRNRV DLKLVFQEGV SAEIQQINIV G NHAFTTDE LISHFQLRDE VPWWNVVGDR KYQKQKLAGD LETLRSYYLD RGYARFNIDS TQVSLTPDKK GIYVTVNITE GD QYKLSGV EVSGNLAGHS AEIEQLTKIE PGELYNGTKV TKMEDDIKKL LGRYGYAYPR VQSMPEINDA DKTVKLRVNV DAG NRFYVR KIRFEGNDTS KDAVLRREMR QMEGAWLGSD LVDQGKERLN RLGFFETVDT DTQRVPGSPD QVDVVYKVKE RNTG SFNFG IGYGTESGVS FQAGVQQDNW LGTGYAVGIN GTKNDYQTYA ELSVTNPYFT VDGVSLGGRL FYNDFQADDA DLSDY TNKS YGTDVTLGFP INEYNSLRAG LGYVHNSLSN MQPQVAMWRY LYSMGEHPST SDQDNSFKTD DFTFNYGWTY NKLDRG YFP TDGSRVNLTG KVTIPGSDNE YYKVTLDTAT YVPIDDDHKW VVLGRTRWGY GDGLGGKEMP FYENFYAGGS STVRGFQ SN TIGPKAVYFP HQASNYDPDY DYECATQDGA KDLCKSDDAV GGNAMAVASL EFITPTPFIS DKYANSVRTS FFWDMGTV W DTNWDSSQYS GYPDYSDPSN IRMSAGIALQ WMSPLGPLVF SYAQPFKKYD GDKAEQFQFN CGKTW

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 39.77923 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #3: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.298109 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #4: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.713676 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.28841 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQT LTLTFNSSGV LTNIDNKPA LSGN

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: Maltose/maltodextrin-binding periplasmic protein,Autotransporter ...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Autotransporter protein EspP translocator
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157 (bacteria)
Molecular weightTheoretical: 60.668305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 KDKDYNPLIG RTGCDVGKSF SGKDWKVTAR AGLGY QFDL LANGETVLRD ASGEKRIKGE KDSRMLMSVG LNAEIRDNVR FGLEFEKSAF GKYNVDNAVN ANFRYSF

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Serine protease EspP

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.47 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92335

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