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- EMDB-18046: Wait Complex: BAM bound Darobactin-B and Extended SurA -

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Basic information

Entry
Database: EMDB / ID: EMD-18046
TitleWait Complex: BAM bound Darobactin-B and Extended SurA
Map data
Sample
  • Complex: Wait Complex: BAM bound Darobactin-B and Extended SurA
    • 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: Chaperone SurA
    • Protein or peptide: Darobactin-B
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsOuter Membrane / Complex / Chaperone / Protein Folding / Inhibitor / MEMBRANE PROTEIN
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / peptide binding / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / peptide binding / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / protein stabilization / response to antibiotic / cell surface / identical protein binding / membrane
Similarity search - Function
Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA 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 ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / : / PPIC-type PPIASE domain / Trigger factor/SurA 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 / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / Outer membrane protein assembly factor BamA / PPIC-type PPIASE domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / 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 / Quinoprotein alcohol dehydrogenase-like superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 BamA / Chaperone SurA / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Photorhabdus heterorhabditis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFenn KL / Ranson NA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P018491/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Outer membrane protein assembly mediated by BAM-SurA complexes.
Authors: Katherine L Fenn / Jim E Horne / Joel A Crossley / Nils Böhringer / Romany J Horne / Till F Schäberle / Antonio N Calabrese / Sheena E Radford / Neil A Ranson /
Abstract: The outer membrane is a formidable barrier that protects Gram-negative bacteria against environmental threats. Its integrity requires the correct folding and insertion of outer membrane proteins ...The outer membrane is a formidable barrier that protects Gram-negative bacteria against environmental threats. Its integrity requires the correct folding and insertion of outer membrane proteins (OMPs) by the membrane-embedded β-barrel assembly machinery (BAM). Unfolded OMPs are delivered to BAM by the periplasmic chaperone SurA, but how SurA and BAM work together to ensure successful OMP delivery and folding remains unclear. Here, guided by AlphaFold2 models, we use disulphide bond engineering in an attempt to trap SurA in the act of OMP delivery to BAM, and solve cryoEM structures of a series of complexes. The results suggest that SurA binds BAM at its soluble POTRA-1 domain, which may trigger conformational changes in both BAM and SurA that enable transfer of the unfolded OMP to the BAM lateral gate for insertion into the outer membrane. Mutations that disrupt the interaction between BAM and SurA result in outer membrane assembly defects, supporting the key role of SurA in outer membrane biogenesis.
History
DepositionJul 27, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18046.png

Downloads & links

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Map

FileDownload / File: emd_18046.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0153
Minimum - Maximum-0.048820864 - 0.086974025
Average (Standard dev.)0.00011154491 (±0.001879729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18046_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wait Complex: BAM bound Darobactin-B and Extended SurA

EntireName: Wait Complex: BAM bound Darobactin-B and Extended SurA
Components
  • Complex: Wait Complex: BAM bound Darobactin-B and Extended SurA
    • 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: Chaperone SurA
    • Protein or peptide: Darobactin-B
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Wait Complex: BAM bound Darobactin-B and Extended SurA

SupramoleculeName: Wait Complex: BAM bound Darobactin-B and Extended SurA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 KDa

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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: 88.460688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVCVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF QEGVSAEIQQ I NIVGNHAF ...String:
AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVCVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP RNRVDLKLVF QEGVSAEIQQ I NIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NIDSTQVSLT PDKKGIYVTV NI TEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYPRVQSMPE INDADKTVKL RVN VDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDTDTQRVP GSPDQVDVVY KVKE RNTGS FNFGIGYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTVDGVSL GGRLFYNDFQ ADDAD LSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSDQDNS FKTDDFTFNY GWTYNK LDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDGLGG KEMPFYENFY AGGSSTV RG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFITPT PFISDKYANS VRTSFFWD M GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLG PLVFSYAQPF KKYDGDKAEQ FQFNIGKTW

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: 39.882375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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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: 34.40125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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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: 25.816818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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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: 11.610833 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
CSTLERVVYR PDINQGNYLT ANDVSKIRVG MTQQQVAYAL GTPLMSDPFG TNTWFYVFRQ QPGHEGVTQQ TLTLTFNSSG VLTNIDNKP ALSGNGGHHH HHHHH

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: Chaperone SurA

MacromoleculeName: Chaperone SurA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.36427 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSSGENLYF QGAPQVVDCV AAVVNNGVVL ESDVDGLMQS VKLNAAQARQ QLPDDATLR HQIMERLIMD QIILQMGQKM GVKISDEQLD QAIANIAKQN NMTLDQMRSR LAYDGLNYNT YRNQIRKEMI I SEVRNNEV ...String:
GSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSSGENLYF QGAPQVVDCV AAVVNNGVVL ESDVDGLMQS VKLNAAQARQ QLPDDATLR HQIMERLIMD QIILQMGQKM GVKISDEQLD QAIANIAKQN NMTLDQMRSR LAYDGLNYNT YRNQIRKEMI I SEVRNNEV RRRITILPQE VESLAQQVGN QNDASTELNL SHILIPLPEN PTSDQVNEAE SQARAIVDQA RNGADFGKLA IA HSADQQA LNGGQMGWGR IQELPGIFAQ ALSTAKKGDI VGPIRSGVGF HILKVNDLRG ESKNISVTEV HARHILLKPS PIM TDEQAR VKLEQIAADI KSGKTTFAAA AKEFSQDPGS ANQGGDLGWA TPDIFDPAFR DALTRLNKGQ MSAPVHSSFG WHLI ELLDT RNVDKTDAAQ KDRAYRMLMN RKFSEEAASW MQEQRASAYV KILSN

UniProtKB: Chaperone SurA

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Macromolecule #7: Darobactin-B

MacromoleculeName: Darobactin-B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus heterorhabditis (bacteria)
Molecular weightTheoretical: 1.055189 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
WN(UX8)TKRF

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6357 / Average electron dose: 39.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 555616
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 164058
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7nri

source_name: PDB, initial_model_type: experimental model

8pz2

chain_id: F, source_name: PDB, initial_model_type: experimental model

7p1c

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 82
Output model

PDB-8pzv:
Wait Complex: BAM bound Darobactin-B and Extended SurA

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