Table I

Summary of cross-linked peptides found in the NDC80 complex

Nter, N terminus; L, light; H, heavy; underlined, site of linkage.

Cross-linkPeptide αPeptide βProtein 1Protein 2Residue αResidue βAlternative residues αAlternative residues βNo. of observationsm/zaErrorazaScoreaModifi-cationsaCross-linka
ppm
ISQDVNKQGLYTPQTKNter-GPLGSMETLSF-qPRNDC80NUF226−5b1803.15020.2451Oxidation (Met)L
IINter-GPLGSMETLSFPRNKILTGADGKNUF2NUF2−5b211840.43382.3363Oxidation (Met)L
IIINter-GPLGSMETLSFPRAKRNUF2NUF2−5b1151930.98742.2233L
IVILTGADGKNLTKKVSLFGKNUF2NDC8029531526.80580.0417L
VLSINKPTSERKVSLFGKNDC80NDC8047531505.28770.4428L
VIIFKDLGYPFALSKVSLFGKRNDC80NDC80156595600.83860.0430L
VIIEKEPNRLESLRKLKNDC80NDC80288298NDC80 Lys-421; NUF2 Lys-3384371.6145−0.5543L
VIIIEKEPNRKLKNDC80NDC80288298NDC80 Lys-421; NUF2 Lys-3382419.23973.3328L
IXKSNISEKTKRNUF2NUF22132211435.57730.3319L
XIVDSPEKLKEKMKNUF2NUF22502575553.641.3324L
XIMKDTVQKLKNARNUF2NUF22592661388.22230.3420H
XIILQNIIDNQKYSVADIERLKNYKNDC80NUF23602521696.62750.3437H
XIIIcKEKLATAQFKLKNARNUF2NUF2351/3492664930.536−2.9224L
XIVAQVYVPLKELLNETEEE-INKKIQDLSDNRNDC80NUF24622993709.37121.3558L
XVTLKEEVQKKLKNDC80NDC80504421NDC80 Lys-298; NUF2 Lys-3384365.21990.1420L
XVITEENSFKRKEKNUF2NUF23423491505.2646−0.1317H
XVIITLKEEVQKLMIVKKNDC80NUF25043482455.01731.3420Oxidation (Met)L
XVIIITLKEEVQKLDDLYQQKKEKNDC80NUF2504/5093493621.09020.2427H
XIXVTTINQEIQKIKNter-GPLGSMAAFRNUF2SPC24400−5b6630.85131.6439H
XXNter-GPLGSMAAFRKVGNNLQRSPC24NDC80−5b5772682.69122.1342Oxidation (Met)L
XXILKSQEIFLNLKNter-GPLGSMAAFRNUF2SPC24418−5b12812.1133.4389L
XXIINter-VEDELALFDKEKLKSPC25NUF214162598.99440.7326H
XXIIIEILTMEKEVAQSLLNAKLSVKLKSPC24SPC2560501680.64240.5443Oxidation (Met)H
XXIVLKEEERKATLIKSPC25NDC80526332393.73070.4434L
XXVKDNLLKLIAEVKLKASLLQLTRSPC25SPC2484982657.16110.3464H
XXVIETISTANKANAERLKRSPC25SPC251221291480.76680.3421H
  • a Data given for the observation with the best match. The data for all observations can be found in Supplemental Table 1. The annotated spectrum of the best observation can be found for all cross-links in Supplemental Fig. 2.

  • b Numbering refers to a linker region (sequence GPLGS, numbered −5 to −1) that precedes the natural N terminus of NUF2 or SPC24 (numbered 1) and that is retained at the N termini of these proteins after proteolytic cleavage from the GST tag used for purification.

  • c The data equally support the N-terminal lysine of the α-peptide being the N-terminal residue in the β-peptide: EKLATAQFK and KLKNAR.