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

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Basic information

Entry
Database: PDB / ID: 8pzv
TitleWait Complex: BAM bound Darobactin-B and Extended SurA
Components
  • (Outer membrane protein assembly factor ...) x 5
  • Chaperone SurA
  • Darobactin-B
KeywordsMEMBRANE PROTEIN / Outer Membrane / Complex / Chaperone / Protein Folding / Inhibitor
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / peptide binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cell outer membrane / unfolded protein binding / protein folding ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / peptide binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cell outer membrane / 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 / Outer membrane protein assembly factor BamE domain / Outer membrane lipoprotein / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / BamE-like / PPIC-type PPIASE domain / Outer membrane protein assembly factor BamA / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Pyrrolo-quinoline quinone repeat / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Outer membrane protein assembly factor BamB / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFenn, K.L. / Ranson, N.A.
Funding support United Kingdom, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE
F: Chaperone SurA
I: Darobactin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,6168
Polymers250,5917
Non-polymers241
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE

#1: Protein Outer membrane protein assembly factor BamA


Mass: 88460.688 Da / Num. of mol.: 1 / Mutation: R76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yaeT / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPJ2
#2: Protein Outer membrane protein assembly factor BamB


Mass: 39882.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 34401.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02
#5: Protein Outer membrane protein assembly factor BamE


Mass: 11610.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A937

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Protein / Protein/peptide , 2 types, 2 molecules FI

#6: Protein Chaperone SurA / Peptidyl-prolyl cis-trans isomerase SurA / PPIase SurA / Rotamase SurA


Mass: 49364.270 Da / Num. of mol.: 1 / Mutation: K27C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: surA, A5U30_000417, A6592_03605, A8499_002794, ACN68_05440, ACN81_29145, ACU57_16255, APX88_24220, AT845_001324, AW119_13300, B6R31_002582, B6R48_000839, B6R87_000840, BANRA_00528, BANRA_01018, ...Gene: surA, A5U30_000417, A6592_03605, A8499_002794, ACN68_05440, ACN81_29145, ACU57_16255, APX88_24220, AT845_001324, AW119_13300, B6R31_002582, B6R48_000839, B6R87_000840, BANRA_00528, BANRA_01018, BEA19_04085, BF481_004290, BG944_001984, BGM66_001952, BHS81_26485, BJJ90_21940, BK292_13085, BKL28_001197, BLM69_001589, BMT50_04585, BMT91_01940, BR158_000614, BTB68_000355, BTQ06_18380, BUO55_001391, BvCmsKKP061_01745, BZL69_04055, C0P57_001694, C1Q91_003811, C2121_001316, C2M16_10200, C3F40_12855, C5N07_07955, C9E67_25835, CA593_03485, CDL36_07310, CDL37_17400, CG831_000934, CIG67_13395, CO706_22450, CQ986_004187, CR539_04305, CR628_002058, CTR35_001670, CV83915_01522, CWS33_09005, CX938_000345, CY655_00285, D0X26_10040, D1912_21775, D3G36_11615, D4M65_00765, D4N09_07440, D4U49_01240, D9D43_02885, D9E49_02755, D9H94_05700, D9J03_00755, D9J61_12370, DIV22_05655, DN627_12350, DNX30_02900, DTL43_06535, DTL90_09105, DTM45_12025, DU321_03070, E3N34_04470, E4K51_06380, E6D34_01565, EA239_14020, EA435_08765, EAN77_10025, EAX79_06120, EC95NR1_04234, ECs0058, EHD79_22565, EIA08_05735, EIZ93_17205, EKI52_11105, EL79_3817, ELT17_00670, ELT48_11535, ELX68_06585, ELX76_13990, ELX79_04690, ELX96_10420, ELY41_07160, ELY48_06875, EN85_002060, EPS76_03390, ERS085406_00448, EWK56_14290, ExPECSC038_04106, F7F11_02675, F7N46_19240, F9413_03830, F9461_05400, F9B07_04095, F9S83_02850, FDM60_06450, FEJ01_07820, FGG80_06585, FIJ20_19845, FOI11_013430, FOI11_22250, FPI65_00225, FV293_03480, FVB16_09095, FWK02_18595, FZN31_20565, FZU14_06355, G3565_16750, G3V95_03015, G3W53_01110, G4A38_11150, G4A47_11380, G5603_15345, G9448_10675, GAI89_10860, GAJ12_06520, GIB53_04680, GJO56_10100, GKF66_03090, GKF89_01900, GNW61_12000, GOP25_07820, GP711_08940, GP944_03700, GP965_09440, GP975_22750, GP979_10530, GQM04_12825, GQM13_12060, GQM21_07395, GQN34_16775, GQW07_13210, GRC73_18725, GRO95_10090, GRW05_16045, GRW24_13500, GRW56_13455, GRW57_14615, GSM54_09305, GSY44_00750, GUC01_17310, GUI33_00795, H0O51_20265, H0O72_17885, H6Y26_001822, HEP30_002160, HI055_000895, HIE29_002974, HJQ60_000806, HKA49_001764, HL563_03315, HL601_07110, HLV18_10235, HLX92_13665, HLZ50_07545, HMV95_05180, HMW38_11180, HV109_19955, HV209_00970, HVV39_17010, HVW04_10815, HVW43_12350, HVY77_21755, HX136_21205, I6H00_14710, I6H02_17995, IA00_000150, IFB95_000673, IH772_13845, IT029_002058, J0541_002446, J5U05_003209, JFD_01141, JNP96_04445, NCTC10082_01513, NCTC10089_04202, NCTC10090_02285, NCTC10429_04362, NCTC10764_05914, NCTC10767_03826, NCTC11181_01494, NCTC11341_03450, NCTC12950_04545, NCTC13127_05582, NCTC13216_02604, NCTC4450_01178, NCTC7922_05670, NCTC7927_04626, NCTC7928_04436, NCTC8009_07508, NCTC8333_04884, NCTC8621_04322, NCTC8622_02500, NCTC8959_04718, NCTC8960_01679, NCTC8985_03282, NCTC9001_05253, NCTC9075_05641, NCTC9077_05259, NCTC9111_04380, NCTC9117_05211, NCTC9702_04913, NCTC9706_01539, NCTC9777_00592, RG28_04480, SAMEA3472056_01091, SAMEA3472147_00263, SAMEA3751407_02555, SAMEA3752557_00759, SAMEA3753106_01622, TUM18780_37170, WR15_01755
Production host: Escherichia coli (E. coli) / References: UniProt: C3TR42, peptidylprolyl isomerase
#7: Protein/peptide Darobactin-B


Mass: 1055.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus heterorhabditis (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wait Complex: BAM bound Darobactin-B and Extended SurA
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6357
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF ChimeraXmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIX1.19.2_4158:0000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 555616
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164058 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 82 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDChain-ID
17NRI

7nri

7NRI1
28PZ2

8pz2

F8PZ22F
37P1C

7p1c

7P1C3
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413574
ELECTRON MICROSCOPYf_angle_d0.62718429
ELECTRON MICROSCOPYf_dihedral_angle_d5.4791867
ELECTRON MICROSCOPYf_chiral_restr0.0452017
ELECTRON MICROSCOPYf_plane_restr0.0042431

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