[English] 日本語
Yorodumi
- EMDB-26107: BamABCDE bound to substrate EspP class 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26107
TitleBamABCDE bound to substrate EspP class 4
Map dataBAM-MBP-76EspP class 4
Sample
  • Complex: BamABCDE bound to substrate EspP class 4
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP 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 BamE
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamC
Keywordsmembrane protein folding / membrane dynamics / outer membrane protein / BAM / beta-barrel / MEMBRANE PROTEIN
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 / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / detection of maltose stimulus / maltose transport complex / protein insertion into membrane / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / 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
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 / Autotransporter, pectate lyase C-like 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 / 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 / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Pyrrolo-quinoline quinone beta-propeller repeat / Omp85 superfamily domain / beta-propeller repeat / Pectin lyase fold/virulence factor / 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 / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Maltose/maltodextrin-binding periplasmic protein / Serine protease EspP / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDoyle MT / Jimah JR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK052037 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK060100 United States
CitationJournal: 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
DepositionJan 31, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26107.png

Downloads & links

-
Map

FileDownload / File: emd_26107.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBAM-MBP-76EspP class 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 257.717 Å		1.07 Å/pix.
x 240 pix.
= 257.717 Å		1.07 Å/pix.
x 240 pix.
= 257.717 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07382 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-2.1351426 - 2.7339728
Average (Standard dev.)0.007101305 (±0.05597144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 257.7168 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : BamABCDE bound to substrate EspP class 4

EntireName: BamABCDE bound to substrate EspP class 4
Components
  • Complex: BamABCDE bound to substrate EspP class 4
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP 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 BamE
    • Protein or peptide: Outer membrane protein assembly factor BamD
    • Protein or peptide: Outer membrane protein assembly factor BamC

-
Supramolecule #1: BamABCDE bound to substrate EspP class 4

SupramoleculeName: BamABCDE bound to substrate EspP class 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Serine protease ...

MacromoleculeName: 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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 83.429984 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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

-
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: 89.750094 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Outer membrane protein assembly factor BamA

-
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 BL21(DE3) (bacteria)
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

UniProtKB: Outer membrane protein assembly factor BamB

-
Macromolecule #4: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.391554 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CSTLERVVYR PDINQGNYLT ANDVSKIRVG MTQQQVAYAL GTPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKP ALSGN

UniProtKB: Outer membrane protein assembly factor BamE

-
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: 25.816818 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Outer membrane protein assembly factor BamD

-
Macromolecule #6: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.40125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Outer membrane protein assembly factor BamC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148165
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more