Table 1. Interprotein Cross-Linked Peptides from Proteins Involved in Transcription and Translation.

mass (Da)	sequence peptide A	Uniprot entry name	position XL residue	sequence peptide B	Uniprot entry name	position XL residue	(template) PDB file model	distance (Å) in structure model
1788.0	XSLEEVK	RPOA	294	XSLEEVK	RPOA	294		n.a.
2194.2	IXELGPR	RSPB	112	DTXLGPEEITR	RPOB	803		n.a.
2298.2	MYLXEIGR	SIGA	107	QLLSEXEYR	RPOC	153	4IGC	16.1
2527.4	LLTVXIPVR	GUDB	52	XDVVDEVYDQR	NUSA	62		n.a.
2629.4	IGAEVXDGDLLVGK	RPOB	837	GYTPADANXR	RPOA	155	2O5I$	12.3
2672.5	XLALK	RPOA	84	VAVAANSLXNVTFTEEQR	RPOC	545	2O5I$	20.0
2762.5	AQEXVFPMTAEGK	GREA	5	XGFTATVIPNR	RPOB	156	4WQT	n.a.
2974.6	DTXLGPEEITR	RPOB	803	TLXPEKDGLFCER	RPOC	40	2O5I$	12.7
3026.6	XGFTATVIPNR	RPOB	156	DXQQEIVVQGAVETR	RPOC	987	2O5I$	21.1
3066.7	IAAQTAXQVVTQR	NUSA	111	VTPXGVTELTAEER	RPOB	849		n.a.
3387.6	VTPXGVTELTAEER	RPOB	849	IFGPTXDWECHCGK	RPOC	56	2O5I$	14.4
3510.8	LVPAGTGMMXYR	RPOC	1179	ALEEIDAGLLSFEXEDRE	RPOZ	63	2O5I$	13.8
3780.0	XEELGDR	RPOE	48	VIDAGDTDVLPGTLLDIHQFTEANXK	RPOC	1104		n.a.
4572.3	GILAKPLXEGTETIER	RPOC	830	SFGDLSENSEYDSAXEEQAFVEGR	GREA	55	4WQT	28.0
4695.7	IGAEVXDGDLLVGK	RPOB	837	GYTPADANXRDDQPIGVIPIDSIYTPVSR	RPOA	155	2O5I$	12.3
6461.1	DTXLGPEEITR	RPOB	803	EILXIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLK	SIGA	258	4IGC	11.6
1694.0	VIXVVR	RL7	73	GPXGELTR	RL6	31		n.a.
1838.1	XEVVQLK	RS2	132	GEVLPTXK	RS3	210	3J9W	22.3
1947.0	DIIDXLK	RS13	62	QXFASADGR	RL31	48		n.a.
2083.2	GXILPR	RS18	43	SVSXTGTLQEAR	RS21	25		n.a.
2217.2	XFVSER	RS18	36	IDPSXLELEER	RS5	8	3J9W	86.2
2383.4	XAVIER	RS6	20	ILDQSAEXIVETAK	RS10	24	3J9W	149.7
2392.3	AEDVAXLR	RS5	155	VFLXYGQNNER	RS8	65	3J9W	12.4
2429.3	XNEEGGK	RS3	212	ILDQSAEXIVETAK	RS10	24	3J9W	<20.9*
2433.3	XFVSER	RS18	36	ILDQSAEXIVETAK	RS10	24	3J9W	116.1
2438.3	GEVLPTXK	RS3	210	VXVLDVNENEER	RS1H	326		n.a.
2457.3	ILDQSAEXIVETAKR	RS10	24	NEEGGX	RS3	218		n.a.
2498.5	XALNSLTGK	RS3	88	VXVLDVNENEER	RS1H	326		n.a.
2500.3	GIVTXVEDK	RS1H	25	QAQDSVXEEAQR	RS2	81		n.a.
2539.4	GEVLPTXK	RS3	210	ILDQSAEXIVETAK	RS10	24	3J9W	18.5
2557.4	XKNEEGGK	RS3	211	ILDQSAEXIVETAK	RS10	24	3J9W	16.9
2571.4	XALNSLTGK	RS3	88	XQAQDSVKEEAQR	RS2	74	3J9W	87.4
2654.4	EITGLGLXEAK	RL7	84	XAAGIESGSGEPNR	RL11	81		n.a.
2701.6	VVXVVK	RL11	7	MLVITPYDXTAIGDIEK	RRF	72		n.a.
2725.4	GPQAANVTXEA	CSPB	65	XQAQDSVKEEAQR	RS2	74		n.a.
2728.5	SVSXTGTLQEAR	RS21	25	IDPSXLELEER	RS5	8		n.a.
2733.4	XNESLEDALR	RS21	8	XLSEYGLQLQEK	RS4	43		n.a.
2739.4	YEVGEGIEXR	EFTS	278	AEVYVLSXEEGGR	EFTU	316	1EFU	18.6
2749.4	ELVDNTPXPLK	RL7	95	XAAGIESGSGEPNR	RL11	81		n.a.
2845.5	AXLSGTAERPR	RL18	21	GGDDTLFAXIDGTVK	RL28	70		n.a.
2861.5	XNESLEDALR	RS21	8	XKLSEYGLQLQEK	RS4	42		n.a.
2881.5	IDPSXLELEER	RS5	8	VXVLSVDRDNER	RS1H	240		n.a.
2882.6	IAXIEVVR	RL19	83	XLLDYAEAGDNIGALLR	EFTU	266		n.a.
3080.6	VHINILEIXR	RS3	106	ELEETPXADQEDYR	RS1H	349		n.a.
3153.8	EAXELVDNTPKPLK	RL7	87	LALETGTAFIEXR	MTNK	377		n.a.
3184.7	XQAQDSVKEEAQR	RS2	74	ILDQSAEXIVETAK	RS10	24	3J9W	75.4
3427.8	EAXELVDNTPKPLK	RL7	87	SLLGNMVEGVSXGFER	RL6	82		n.a.
3524.8	VNITIHTAXPGMVIGK	RS1	71	ELEETPXADQEDYR	RS1H	349		n.a.
3789.9	EAXELVDNTPKPLK	RL7	87	AXEAEAAGADFVGDTDYINK	RL1	85		n.a.

^aX, cross-linked K residue; *, linked residue K212 (RS3) is not in structure model; distance is assumed based on a maximal distance of 4 Å between Cα atoms of K211 and K212; $, the structure of the RNAP elongation complex was modeled as described in the Experimental Procedures; n.a., model not available or linked residue not in structure. Uniprot entry names RPOA, RPOB, RPOC, RPOE, and RPOZ correspond to subunits α, β, β′, δ, and ω of RNAP.