7P47

Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (B)	Structural maintenance of chromosomes protein 5	polymer	84	9978.6	1	UniProt (Q08204)	Saccharomyces cerevisiae (Baker's yeast)
2	B (C)	SUMO-conjugating enzyme UBC9	polymer	165	19071.6	1	UniProt (P50623) Pfam (PF00179)	Saccharomyces cerevisiae (Baker's yeast)	RING-type E3 SUMO transferase UBC9,Ubiquitin carrier protein 9,Ubiquitin-conjugating enzyme E2-18 kDa,Ubiquitin-protein ligase
3	C (A)	E3 SUMO-protein ligase MMS21	polymer	214	24117.1	1	UniProt (P38632) Pfam (PF22326) Pfam (PF11789)	Saccharomyces cerevisiae (Baker's yeast)	E3 SUMO-protein transferase MMS21,Methyl methanesulfonate-sensitivity protein 21,Non-structural maintenance of chromosome element 2,Non-SMC element 2
4	D, E (E, D)	Ubiquitin-like protein SMT3	polymer	121	13739.4	2	UniProt (Q12306) Pfam (PF00240)	Saccharomyces cerevisiae (Baker's yeast)
5	F (A)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)

Sequence modifications

B: 737 - 777 (UniProt: Q08204)

PDB	External Database	Details
Met 326	-	initiating methionine
Gly 327	-	expression tag
Thr 328	-	expression tag
Asp 329	-	expression tag
Glu 330	-	expression tag
Phe 331	-	expression tag
Leu 332	-	expression tag
Lys 333	-	expression tag
Ala 334	-	expression tag
Lys 335	-	expression tag
Glu 336	-	expression tag
Lys 337	-	expression tag
Ile 338	-	expression tag
Asn 339	-	expression tag
Glu 340	-	expression tag
Ile 341	-	expression tag
Phe 342	-	expression tag
Glu 343	-	expression tag
Lys 344	-	expression tag
Leu 345	-	expression tag
Asn 346	-	expression tag
Thr 347	-	expression tag
Ile 348	-	expression tag
Arg 349	-	expression tag
Asp 350	-	expression tag
Glu 351	-	expression tag
Val 352	-	expression tag
Ile 353	-	expression tag
Lys 354	-	expression tag
Lys 355	-	expression tag
Lys 356	-	expression tag
Asn 357	-	expression tag
Gln 358	-	expression tag
Asn 359	-	expression tag
Glu 360	-	expression tag
Tyr 361	-	expression tag
Tyr 362	-	expression tag
Arg 363	-	expression tag
Gly 732	-	expression tag
Arg 733	-	expression tag
Thr 734	-	expression tag
Gly 735	-	expression tag
Thr 736	-	expression tag

C: 1 - 157 (UniProt: P50623)

PDB	External Database	Details
Lys 129	Ala 129	engineered mutation
Arg 153	Lys 153	engineered mutation
Gly 158	-	expression tag
Tyr 159	-	expression tag
His 160	-	expression tag
His 161	-	expression tag
His 162	-	expression tag
His 163	-	expression tag
His 164	-	expression tag
His 165	-	expression tag

A: 27 - 267 (UniProt: P38632)

PDB	External Database	Details
Met 4	-	initiating methionine
Gly 5	-	expression tag
Ser 6	-	expression tag
Ser 7	-	expression tag
His 8	-	expression tag
His 9	-	expression tag
His 10	-	expression tag
His 11	-	expression tag
His 12	-	expression tag
His 13	-	expression tag
Ser 14	-	expression tag
Ser 15	-	expression tag
Gly 16	-	expression tag
Leu 17	-	expression tag
Val 18	-	expression tag
Pro 19	-	expression tag
Arg 20	-	expression tag
Gly 21	-	expression tag
Ser 22	-	expression tag
His 23	-	expression tag
Met 24	-	expression tag
Leu 25	-	expression tag
Glu 26	-	expression tag
-	Phe 83	deletion
-	Asp 84	deletion
-	Glu 85	deletion
-	His 86	deletion
-	Ile 87	deletion
-	Lys 88	deletion
-	Asp 89	deletion
-	Leu 90	deletion
-	Lys 91	deletion
-	Lys 92	deletion
-	Asn 93	deletion
-	Phe 94	deletion
-	Lys 95	deletion
-	Gln 96	deletion
-	Ser 97	deletion
-	Ser 98	deletion
-	Asp 99	deletion
-	Ala 100	deletion
-	Cys 101	deletion
-	Pro 102	deletion
-	Gln 103	deletion
-	Ile 104	deletion
-	Asp 105	deletion
-	Leu 106	deletion
-	Ser 107	deletion
-	Thr 108	deletion
-	Trp 109	deletion
-	Asp 110	deletion
-	Lys 111	deletion
-	Tyr 112	deletion
-	Arg 113	deletion
-	Thr 114	deletion
-	Gly 115	deletion
-	Glu 116	deletion
-	Leu 117	deletion
-	Thr 118	deletion
-	Ala 119	deletion
-	Pro 120	deletion
-	Lys 121	deletion
-	Leu 122	deletion
-	Ser 123	deletion
-	Glu 124	deletion
-	Leu 125	deletion
-	Tyr 126	deletion
-	Leu 127	deletion
-	Asn 128	deletion
-	Met 129	deletion
-	Pro 130	deletion
-	Thr 131	deletion
-	Pro 132	deletion
Gly 133	Glu 133	conflict
Thr 134	Pro 134	conflict

E, D: 1 - 98 (UniProt: Q12306)

PDB	External Database	Details
Met -22	-	initiating methionine
Gly -21	-	expression tag
Ser -20	-	expression tag
Ser -19	-	expression tag
His -18	-	expression tag
His -17	-	expression tag
His -16	-	expression tag
His -15	-	expression tag
His -14	-	expression tag
His -13	-	expression tag
Ser -12	-	expression tag
Ser -11	-	expression tag
Gly -10	-	expression tag
Leu -9	-	expression tag
Val -8	-	expression tag
Pro -7	-	expression tag
Arg -6	-	expression tag
Gly -5	-	expression tag
Ser -4	-	expression tag
His -3	-	expression tag
Met -2	-	expression tag
Ala -1	-	expression tag
Ser 0	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	5
	Total formula weight	80646.2
Non-Polymers*	Number of molecules	1
	Total formula weight	65.4
All*	Total formula weight	80711.6

*Water molecules are not included.