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- PDB-9cnz: Structure of BAM complexed with PTB2 ligand in detergent -

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Basic information

Entry
Database: PDB / ID: 9cnz
TitleStructure of BAM complexed with PTB2 ligand in detergent
Components
  • (Outer membrane protein assembly factor ...) x 5
  • PTB2 circular peptide
KeywordsMEMBRANE PROTEIN / protein structure / circular peptide
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / identical protein binding / membrane
Similarity search - Function
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 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 / 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 / Quinoprotein alcohol dehydrogenase-like 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 BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSun, D. / Tegunov, D. / Payandeh, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: The discovery and structural basis of two distinct state-dependent inhibitors of BamA.
Authors: Dawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K ...Authors: Dawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K Murchison / Stephanie Shriver / Christine Tam / Hiroshi Ijiri / Hiroko Inaba / Tatsuya Sano / Hayato Yanagida / Junichi Nishikawa / Christopher E Heise / Wayne J Fairbrother / Man-Wah Tan / Nicholas Skelton / Wendy Sandoval / Benjamin D Sellers / Claudio Ciferri / Peter A Smith / Patrick C Reid / Christian N Cunningham / Steven T Rutherford / Jian Payandeh /
Abstract: BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of ...BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
G: PTB2 circular peptide
H: PTB2 circular peptide
I: PTB2 circular peptide


Theoretical massNumber of molelcules
Total (without water)216,8848
Polymers216,8848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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 / Omp85


Mass: 90643.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamB


Mass: 41918.945 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: 36875.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: W8SZY2
#4: Protein Outer membrane protein assembly factor BamD


Mass: 27858.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYV7
#5: Protein Outer membrane protein assembly factor BamE


Mass: 13530.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: bamE, smpA, smpA_1, smpA_2, A5U30_004761, A8502_003118, ACN81_10110, ACU57_00040, AW118_18475, AWP47_02615, B6R15_004158, B6R31_004759, BANRA_01160, BANRA_03480, BE932_10900, BER14_21305, BG944_ ...Gene: bamE, smpA, smpA_1, smpA_2, A5U30_004761, A8502_003118, ACN81_10110, ACU57_00040, AW118_18475, AWP47_02615, B6R15_004158, B6R31_004759, BANRA_01160, BANRA_03480, BE932_10900, BER14_21305, BG944_004822, BGM66_003581, BGZ_03322, BGZ_03360, BJI68_04965, BK292_15180, BK383_10965, BKL28_002039, BTB68_003672, BTQ06_08460, BvCmsKKP061_02391, BvCmsSIP010_01660, BXT93_22155, C0P57_003578, C1Q91_004646, C2121_004298, C2M16_24735, C2R31_001300, C3F40_23815, C9Z68_21235, CF22_004800, CG704_21595, CIG67_05840, CTR35_004191, CV83915_03496, D3C88_33860, D3G36_24940, D4M65_08385, D4N09_18960, D9D43_23135, D9E49_21045, D9J61_07090, DD762_23945, DIV22_27230, DNQ45_01360, DNX30_24630, DS732_19245, DTL43_21605, DU321_24480, E4K51_10685, E5H86_23265, EAI46_08790, EIA08_06590, EIZ93_15710, EN85_004125, EPS76_07565, EPS97_18785, F7F11_01805, F7N46_20005, F9413_21470, F9461_09705, F9B07_09575, FGAF848_35330, FIJ20_21810, FJQ40_23045, FOI11_00120, FOI11_023060, FORC44_1220, FPI65_16365, FPS11_21880, FVB16_18295, FWK02_09415, FZU14_20455, G3V95_09935, G3W53_10490, G4A38_21000, G4A47_01315, G5603_07570, GAI89_21575, GAJ12_00120, GKF66_23890, GNW61_16365, GOP25_24540, GP711_06005, GP954_12740, GP965_16485, GP975_20410, GQA06_18025, GQE86_17925, GQM04_26375, GQM13_06310, GQM21_13515, GQN34_14130, GQW07_17195, GRC73_20465, GRO95_16555, GRW05_07295, GRW24_17075, GRW56_11330, GRW57_07180, GUC01_18130, H0O72_19885, HEP30_021230, HEP34_004240, HHH44_004392, HI055_003787, HIE29_001466, HJQ60_000025, HLX92_22475, HLZ50_20300, HMV95_03275, HV109_05655, HV209_12725, HVV39_05080, HVW04_21950, HVW43_23255, HVY77_06725, I6H00_24640, I6H02_08695, IFB95_001954, J0541_004271, J5U05_003378, JNP96_20865, KV499_004101, NCTC10082_03668, NCTC10089_01217, NCTC10418_01985, NCTC10429_01977, NCTC10764_00459, NCTC10767_02499, NCTC10865_01545, NCTC10974_01452, NCTC11112_07467, NCTC11126_05233, NCTC11181_03422, NCTC11341_01008, NCTC13148_02470, NCTC7922_00773, NCTC7927_01352, NCTC7928_01496, NCTC8009_02711, NCTC8179_06846, NCTC8333_01395, NCTC8500_01302, NCTC8621_00013, NCTC8621_01206, NCTC8622_03288, NCTC8959_02561, NCTC8960_03971, NCTC8985_06038, NCTC9044_00387, NCTC9045_01444, NCTC9073_04671, NCTC9075_01806, NCTC9077_01597, NCTC9081_05698, NCTC9117_01766, NCTC9702_01479, NCTC9706_03490, NCTC9962_00832, NEP60_26680, OGM49_18410, QDW62_06140, RZR61_19225, SAMEA3472112_00955, WR15_13295
Production host: Escherichia coli (E. coli) / References: UniProt: A0A366UU94

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Protein/peptide , 1 types, 3 molecules GHI

#6: Protein/peptide PTB2 circular peptide


Mass: 2019.381 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has ligand of interestY
Has protein modificationY

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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: BamABCDE complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181444 / Symmetry type: POINT

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