(Taxonomy 83333, downloaded 1 July 2017), known contaminants and
the reversed versions of each sequence. Peptide assignments were
first filtered to a 1% FDR at the peptide level and subsequently to a 2%
FDR at the protein level. Peptide spectral matches (PSMs) per pro-
tein were summed per sample across all fractions from the GelC-MS
experiment. The Statistical Analysis of INTeractome (SAINT) algorithm
(SAINTExpress-spc v.3.6.1)^69 was run with default settings comparing
the sum of PSMs for all identified proteins enriched with each antibody
separately (target) to the combined pool of control purifications (Sup-
plementary Table 12). Interactions with a SAINT score >0.8 and Bayesian
FDR < 0.05 were marked as significant.
Reporting summary
Further information on research design is available in the Nature
Research Reporting Summary linked to this paper.
Data availability
Structural data are deposited in the Protein Data Bank (PDB) under
accession number 6XLP. All mass spectrometry RAW files were
uploaded to the MassIVE data repository, accessible by the identifier
MSV000083754, and can be downloaded from ftp://MSV000083754@
massive.ucsd.edu. DNA sequencing data were deposited at NCBI under
BioProject PRJNA541088, BioSample SAMN11572257, experiment
SRX5788703, run SRR9010525. The E. coli CFT073 reference genome
was deposited at NCBI under BioProject PRJNA624646, BioSample
SAMN14575425, accession CP051263. Source data are provided with
this paper.
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Acknowledgements We thank our Genentech colleagues for their support, in particular,
A. Song, I. Kekessie, J. Toms, E. Hecht, C. Peng, A. Liu, P. Smith, A. Estevez, C. Ciferri, H. Ho,
E. Castellanos, A. K. Katakam, I. Zilberleyb, M. Reichelt, M.-W. Tan, J. Kiefer, Y. Franke, C. Koth,
E. Brown and S. Hymowitz. We thank D. Cawley for antibody generation and Smartox
Biotechnology for peptide synthesis. Use of the Linac Coherent Light Source (LCLS) and the
Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory,
are supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy
Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology
Program is supported by the DOE Office of Biological and Environmental Research, and by the
National Institutes of Health, National Institute of General Medical Sciences (P41GM103393).
The contents of this publication are solely the responsibility of the authors and do not
necessarily represent the official views of NIGMS or NIH. C.G. appreciates support from the
SLAC National Accelerator Laboratory and Stanford University through a Panofsky Fellowship.
All reagents are available under a materials transfer agreement with Genentech.Author contributions T.C. and K.R.B. contributed equally to this work. T.C. purified and
crystallized PbgA, with support from C.L.N. K.R.B., K.M.S., N.N.N., D. Swem and S.T.R.
performed microbiology experiments. Q.L., P.L., E.V., G.H. and W.S. performed proteomics and
lipidomics experiments, with support from T.C. J.R. and E.S. performed genomic sequence
analyses. D. Sangaraju and S.S.-L. performed metabolomics experiments, with support from
T.C. S.P. and M.X. performed in vivo experiments. L.M. and T.D.V. performed molecular biology
and protein expression experiments. A.M. performed the LAL assay. D.P.D., M.S.H. and C.G.
collected and processed SFX data. T.C. and J.P. determined and refined structures, with input
from C.G. B.D.S. performed and analysed molecular dynamics simulations. J.P. proposed the
lipid A-binding potential of PbgA-derived peptides and designed variants; N.S. and E.J.H.
designed key peptides; M.R.-G. synthesized key peptides; T.C. performed lipid-binding
interferometry experiments; K.R.B. and S.T.R. performed bacterial growth inhibition and MIC
assays with peptides. T.C., K.R.B., S.T.R. and J.P. wrote the manuscript with input from all
authors. J.P. and S.T.R. co-supervised the project and E.J.H., J.P. and S.T.R. are co-senior authors.Competing interests All authors, except D.P.D., M.S.H. and C.G., are or were employees of
Genentech/Roche.Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41586-020-
2597-x.
Correspondence and requests for materials should be addressed to E.J.H., J.P. or S.T.R.
Peer review information Nature thanks Bert van den Berg, Russell Bishop, Changjiang Dong
and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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