8PZV

Wait Complex: BAM bound Darobactin-B and Extended SurA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn, K.L.Horne, J.E.Crossley, J.A.Bohringer, N.Horne, R.J.Schaberle, T.F.Calabrese, A.N.Radford, S.E.Ranson, N.A.

(2024) Nat Commun 15: 7612-7612

  • DOI: https://doi.org/10.1038/s41467-024-51358-x
  • Primary Citation of Related Structures:  
    8PZ1, 8PZ2, 8PZU, 8PZV, 8Q0G, 8QP5, 8QPU, 8QPV, 8QPW

  • PubMed 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 (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.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA790Escherichia coliMutation(s): 1 
Gene Names: yaeT
Membrane Entity: Yes 
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A940
Entity Groups  
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UniProt GroupP0A940
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB373Escherichia coliMutation(s): 0 
Gene Names: bamByfgLb2512JW2496
Membrane Entity: Yes 
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
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Go to UniProtKB:  P77774
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UniProt GroupP77774
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC320Escherichia coliMutation(s): 0 
Gene Names: bamCdapXnlpBb2477JW2462
Membrane Entity: Yes 
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A903
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UniProt GroupP0A903
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD226Escherichia coliMutation(s): 0 
Gene Names: bamDyfiOb2595JW2577
Membrane Entity: Yes 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC02
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UniProt GroupP0AC02
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE104Escherichia coliMutation(s): 0 
Gene Names: bamEsmpAb2617JW2598
Membrane Entity: Yes 
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A937
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UniProt GroupP0A937
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone SurA450Escherichia coliMutation(s): 1 
Gene Names: 
surAA5U30_000417A6592_03605A8499_002794ACN68_05440ACN81_29145ACU57_16255APX88_24220AT845_001324AW119_13300B6R31_002582B6R48_000839B6R87_000840BANRA_00528BANRA_01018BEA19_04085BF481_004290BG944_001984BGM66_001952BHS81_26485BJJ90_21940BK292_13085BKL28_001197BLM69_001589BMT50_04585BMT91_01940BR158_000614BTB68_000355BTQ06_18380BUO55_001391BvCmsKKP061_01745BZL69_04055C0P57_001694C1Q91_003811C2121_001316C2M16_10200C3F40_12855C5N07_07955C9E67_25835CA593_03485CDL36_07310CDL37_17400CG831_000934CIG67_13395CO706_22450CQ986_004187CR539_04305CR628_002058CTR35_001670CV83915_01522CWS33_09005CX938_000345CY655_00285D0X26_10040D1912_21775D3G36_11615D4M65_00765D4N09_07440D4U49_01240D9D43_02885D9E49_02755D9H94_05700D9J03_00755D9J61_12370DIV22_05655DN627_12350DNX30_02900DTL43_06535DTL90_09105DTM45_12025DU321_03070E3N34_04470E4K51_06380E6D34_01565EA239_14020EA435_08765EAN77_10025EAX79_06120EC95NR1_04234ECs0058EHD79_22565EIA08_05735EIZ93_17205EKI52_11105EL79_3817ELT17_00670ELT48_11535ELX68_06585ELX76_13990ELX79_04690ELX96_10420ELY41_07160ELY48_06875EN85_002060EPS76_03390ERS085406_00448EWK56_14290ExPECSC038_04106F7F11_02675F7N46_19240F9413_03830F9461_05400F9B07_04095F9S83_02850FDM60_06450FEJ01_07820FGG80_06585FIJ20_19845FOI11_013430FOI11_22250FPI65_00225FV293_03480FVB16_09095FWK02_18595FZN31_20565FZU14_06355G3565_16750G3V95_03015G3W53_01110G4A38_11150G4A47_11380G5603_15345G9448_10675GAI89_10860GAJ12_06520GIB53_04680GJO56_10100GKF66_03090GKF89_01900GNW61_12000GOP25_07820GP711_08940GP944_03700GP965_09440GP975_22750GP979_10530GQM04_12825GQM13_12060GQM21_07395GQN34_16775GQW07_13210GRC73_18725GRO95_10090GRW05_16045GRW24_13500GRW56_13455GRW57_14615GSM54_09305GSY44_00750GUC01_17310GUI33_00795H0O51_20265H0O72_17885H6Y26_001822HEP30_002160HI055_000895HIE29_002974HJQ60_000806HKA49_001764HL563_03315HL601_07110HLV18_10235HLX92_13665HLZ50_07545HMV95_05180HMW38_11180HV109_19955HV209_00970HVV39_17010HVW04_10815HVW43_12350HVY77_21755HX136_21205I6H00_14710I6H02_17995IA00_000150IFB95_000673IH772_13845IT029_002058J0541_002446J5U05_003209JFD_01141JNP96_04445NCTC10082_01513NCTC10089_04202NCTC10090_02285NCTC10429_04362NCTC10764_05914NCTC10767_03826NCTC11181_01494NCTC11341_03450NCTC12950_04545NCTC13127_05582NCTC13216_02604NCTC4450_01178NCTC7922_05670NCTC7927_04626NCTC7928_04436NCTC8009_07508NCTC8333_04884NCTC8621_04322NCTC8622_02500NCTC8959_04718NCTC8960_01679NCTC8985_03282NCTC9001_05253NCTC9075_05641NCTC9077_05259NCTC9111_04380NCTC9117_05211NCTC9702_04913NCTC9706_01539NCTC9777_00592RG28_04480SAMEA3472056_01091SAMEA3472147_00263SAMEA3751407_02555SAMEA3752557_00759SAMEA3753106_01622TUM18780_37170WR15_01755

EC: 5.2.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P0ABZ6 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABZ6
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UniProt GroupP0ABZ6
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  • Reference Sequence

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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Darobactin-BG [auth I]7Photorhabdus heterorhabditisMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UX8
Query on UX8
G [auth I]L-PEPTIDE LINKINGC11 H12 N2 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.19.2_4158:0000

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/P018491/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release