Table 1. Structural analysis of virus-receptor complexes cross-linked with CBDPS at sites identified by tandem mass spectrometry following proteolytic digestion and affinity purification of cross-linked peptides.

The spacer length of CBDPS is 14 Å. Distances are measured from models based on electron microscopy of complexes that were not cross-linked. Thus, the distances do not reflect any chemical constraint imposed by the cross-linker on conformation, or any remodeling of the protein structure.

Virus	Residue	AAVR construct	Residue	Location	Distance	Measured from:
AAVDJ	K556	Full ecto-protein	K404	PKD2 (N-terminal)	13.4 Å	PKD2 modeled into high resolution EM of AAV2-PKD1/2
AAV2	K490	MBP-PKD1-5	K399	PKD1/2 linker	9.9 Å	PKD1 homology model, anchored to PKD2 in above EM
AAV2	T560	MBP-PKD1-5	K399	PKD1/2 linker	17.8 Å	As above
AAV2	K556	MBP-PKD1-5	K338	PKD1	13.8 Å	As above
AAV2	T450	MBP-PKD1-5	K399	PKD1/2 linker	27.7 Å	As above
AAV2	K556	MBP-PKD1-5	K597	PKD3/4 linker		Not attempted