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 9OJ4 | pdb_00009oj4

Mouse LRRC15 extracellular domain in complex with disulfide constrained peptide ML-YSD-07 and Fab-E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OJ4

This is version 1.1 of the entry. See complete history. 

Literature

Development of LRRC15-binding disulfide-constrained peptides for PET imaging of cancer-associated fibroblasts.

Tombling, B.J., Cai, F., Wendorff, T.J., Ogasawara, A., Gill, H.S., Tinianow, J.N., Chang, A., Balana, A.T., Peng, L., Miller, S.E., Walters, B.T., Lictao, A., Yu, Q., DeWitt, D.C., Wei, Y., Wu, S.Z., Sudhamsu, J., Krishnamurty, A.T., Williams, S.P., Marik, J., Zhang, Y., Maun, H.R., Kirchhofer, D.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-73845-z
  • Primary Citation Related Structures: 
    9OIB, 9OJ4

  • PubMed Abstract: 

    Leucine-rich-repeat-containing protein 15 (LRRC15) is selectively expressed on cancer-associated fibroblasts (CAFs) and constitutes a promising biomarker for imaging the tumor microenvironment. Using a combinatorial library approach, assisted by machine learning, we developed disulfide-constrained peptides (DCPs), notably ML-YSD-07 and ML-PD-03, that demonstrate subnanomolar affinities for murine LRRC15 (muLRRC15) and specifically localize onto muLRRC15-expressing fibroblasts. PET imaging with 18 F-radiolabeled ML-YSD-07 exhibits specific tumor accumulation in a murine pancreatic cancer model highly enriched with LRRC15-expressing CAFs. Crystal structures of apo-muLRRC15 and of ML-YSD-07-bound muLRRC15 show that the DCPs evolved to adopt a distinct binding conformation that efficiently interacts with a flat epitope on muLRRC15. Collectively, this work identifies potent, molecularly engineered LRRC15-binding peptides and further highlights LRRC15 as a valuable CAF biomarker for cancer imaging applications.


  • Organizational Affiliation: 
    • Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 103.21 kDa 
  • Atom Count: 7,370 
  • Modeled Residue Count: 920 
  • Deposited Residue Count: 929 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab-E1 light chain214Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab-E1 heavy chain227Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 15458Mus musculusMutation(s): 1 
Gene Names: Lrrc15
UniProt & NIH Common Fund Data Resources
Find proteins for Q80X72 (Mus musculus)
Explore Q80X72 
Go to UniProtKB:  Q80X72
IMPC:  MGI:1921738
Entity Groups
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UniProt GroupQ80X72
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q80X72-1
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ML-YSD-0730synthetic constructMutation(s): 0 
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Reference Sequence

Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.14α = 90
b = 66.601β = 111.582
c = 92.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Database references