Crosslinking methods Protein complex Protein complex Interaction Findings Ref.
Photo-crosslinking UAA in live cells (No MS involved)
CXCR4(GPCR)-T140
Protein- small molecule Protein- small molecule
F189 is important for binding T140 ligand
(Grunbeck et al., 2011)
CCR5(GPCR)-maraviroc
Protein- small molecule Protein- small molecule
New contact residues identified
(Grunbeck et al., 2012)
PGRMC1-Insig-1 Protein-protein Protein-protein New interfaces identified (Suchanek et al., 2005)
AT1R(GPCR)-arrestin Protein-protein Protein-protein Ligand-dependent interface change, newly found intracellular loop engagement in the interface (Gagnon et al., 2019)
Antibody- EGFR Protein-protein Protein-protein Roles of interfacial residues in binding (Bridge et al., 2019)
MurJ-LipidII Protein-lipid Protein-lipid Critical interfacial residues responsible for transient LipidII binding (Rubino et al., 2020)
Photo-crosslinking UAA LptD-LptE Protein-protein Protein-protein Critical interfacial residues (Freinkman et al., 2011)
DegP-substrate Protein-protein Protein-protein New substrates identified by a photoactivatable UAA at the substrate recognition site (He et al., 2017)
Histone H3-various ligands Protein-protein Protein-protein Weak and transient PPIs identified (Yang et al., 2020)
HdeA dimer Protein-protein Protein-protein pH-dependent changes in the dimer interface (Yang et al., 2016)
HdeA - DegP Protein-protein Protein-protein HdeA binding to multiple interfacial regions in DegP
Rho-RTKN Protein-protein Protein-protein RTKN interaction with RohA through a similar binding interface as that on PKN
Photo-crosslinker, cleavable, MS label MAP kinase - MKK4 peptide Protein-peptide Protein-peptide Unique binding interface of an intrinsically disordered peptide within a folded protein domain (Parker et al., 2018)
E6AP(E3) - UbcH7(E2) Protein-protein Protein-protein Previously unrecognized catalytic residues of the E6AP ligase (Krist and Statsyuk 2015)
Photo-crosslinker, heterobifunctional SurA-Unfolded OmpX Protein-protein Protein-protein Multi-site binding of OmpX to SurA (Calabrese et al., 2020)
Sky-OmpA Protein-protein Protein-protein Unique residues and sub-regions involved in transient interaction between Skp and denatured OmpA (Horne et al., 2018)
Photo-activatable cholesterol
GlyR - cholesterol
Protein-lipid
Protein-lipid
Unique cholesterol binding interfaces of GlyR Cholesterol concentration-dependent changes in the interface
(Ferraro and Cascio 2018)
Lys/Asp/Glu-cross-reactive chemical linker Yeast proteasome Protein-protein Protein-protein Dynamic and disordered interface of subunits (RPN2, RPN13) (Mintseris and Gygi 2020)
BAX oligomer Protein-protein Protein-protein The unstructured N terminus and newly exposed α1 of BAX adjacent to one another in the oligomeric state (Hauseman et al., 2020)
Heterobifunctional chemical crosslinker RAP1B-Glycan Protein-glycan Protein-glycan Different contact residues of RAP1B with glycan variants (Xie et al., 2021)
MDA5 filament Protein-protein Protein-protein Configuration of filaments (Wu et al., 2013)
Amine-reactive chemical linker
p53 tetramer
Protein-protein
Protein-protein
DNA-dependent changes in the dimer-dimer interface
(Arlt et al., 2017)
p53 tetramer Protein-protein Protein-protein Flexible C-terminal (Arlt et al., 2015)
NLRP1-DPP9 Protein-protein Protein-protein CLMS data used for validation of the atomic model revealed by the cryo-EM (Hollingsworth et al., 2021)
SLAIN2, CLASP2, ch-TOG Protein-protein Protein-protein SLAIN2 showed crosslink patterns contradictory to previous x-ray crystal structure (Liu et al., 2017)
hIRE1α LD oligomer
Protein-protein
Protein-protein
Critical residues in the oligomeric interface
(Karagöz et al., 2017)
Structure refinement from published dataset
Rpn2-Rpn13
Protein-protein
Protein-protein
The intrinsically disordered C-terminal interface of Rpn2
(Gong et al., 2020)