Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8QCF

yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (B)	Exosome complex component RRP45	polymer	305	34001.9	1	UniProt (Q05636) Pfam (PF01138) Pfam (PF03725)	Saccharomyces cerevisiae (brewer's yeast)
2	B (C)	Exosome complex component SKI6	polymer	249	27892.0	1	UniProt (P46948) Pfam (PF01138) Pfam (PF03725)	Saccharomyces cerevisiae (brewer's yeast)
3	C (D)	Exosome complex component RRP43	polymer	394	44109.0	1	UniProt (P25359) Pfam (PF01138)	Saccharomyces cerevisiae (brewer's yeast)
4	D (E)	RRP46 isoform 1	polymer	226	24659.4	1	UniProt (A0A6A5PYM9) Pfam (PF01138) Pfam (PF03725) UniProt (by SIFTS) (P53256)	Saccharomyces cerevisiae (brewer's yeast)
5	E (F)	Exosome complex component RRP42	polymer	268	29391.5	1	UniProt (Q12277)	Saccharomyces cerevisiae (brewer's yeast)
6	F (G)	Exosome complex component MTR3	polymer	250	27573.9	1	UniProt (P48240) Pfam (PF01138)	Saccharomyces cerevisiae (brewer's yeast)
7	G (H)	Exosome complex component RRP40	polymer	244	26939.7	1	UniProt (Q08285) Pfam (PF21262) Pfam (PF15985) Pfam (PF18311)	Saccharomyces cerevisiae (brewer's yeast)
8	H (I)	Exosome complex component RRP4	polymer	364	39929.7	1	UniProt (P38792) Pfam (PF14382) Pfam (PF21266) Pfam (PF15985)	Saccharomyces cerevisiae (brewer's yeast)	Ribosomal RNA-processing protein 4
9	I (J)	Exosome complex component CSL4	polymer	295	31911.6	1	UniProt (P53859) Pfam (PF21551) Pfam (PF10447)	Saccharomyces cerevisiae (brewer's yeast)
10	J (K)	Exosome complex exonuclease DIS3	polymer	1005	114214.1	1	UniProt (Q08162) Pfam (PF13638) Pfam (PF17216) Pfam (PF17849) Pfam (PF00773) Pfam (PF17215)	Saccharomyces cerevisiae (brewer's yeast)
11	K (L)	Superkiller protein 7	polymer	353	39242.0	1	UniProt (Q08491)	Saccharomyces cerevisiae (brewer's yeast)
12	L (M)	Antiviral helicase SKI2	polymer	1040	117412.7	1	UniProt (P35207) Pfam (PF17911) Pfam (PF00270) Pfam (PF00271) Pfam (PF21408)	Saccharomyces cerevisiae (brewer's yeast)	Superkiller protein 2
13	M (N)	RNA (5'hairpin 60U)	polymer	78	24196.5	1		Saccharomyces cerevisiae
14	N (M)	ADENOSINE-5'-TRIPHOSPHATE	non-polymer		507.2	1	Chemie (ATP)

Sequence modifications

C: 1 - 246 (UniProt: P46948)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
His 0	-	expression tag

D: 1 - 394 (UniProt: P25359)

PDB	External Database	Details
Ser 102	Ala 102	conflict
Met 363	Val 363	conflict

E: 1 - 223 (UniProt: A0A6A5PYM9)

PDB	External Database	Details
Ala -2	-	expression tag
Ala -1	-	expression tag
Ser 0	-	expression tag

F: 1 - 265 (UniProt: Q12277)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
His 0	-	expression tag
Ile 138	Val 138	conflict

G: 1 - 250 (UniProt: P48240)

PDB	External Database	Details
Thr 161	Met 161	conflict

H: 1 - 240 (UniProt: Q08285)

PDB	External Database	Details
Gly -3	-	expression tag
Pro -2	-	expression tag
Asp -1	-	expression tag
Ser 0	-	expression tag

I: 1 - 359 (UniProt: P38792)

PDB	External Database	Details
Thr -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Arg -1	-	expression tag
Ser 0	-	expression tag

J: 1 - 292 (UniProt: P53859)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
His 0	-	expression tag

K: 1 - 1001 (UniProt: Q08162)

PDB	External Database	Details
Gly -3	-	expression tag
Pro -2	-	expression tag
Asp -1	-	expression tag
Ser 0	-	expression tag

L: 1 - 239 (UniProt: Q08491)

PDB	External Database	Details
Gly -105	-	expression tag
Pro -104	-	expression tag
Asp -103	-	expression tag
Ser -102	-	expression tag
Met -101	-	expression tag
Ser -100	-	expression tag
Ala -99	-	expression tag
Gly -98	-	expression tag
Leu -97	-	expression tag
Glu -96	-	expression tag
Val -95	-	expression tag
Leu -94	-	expression tag
Phe -93	-	expression tag
Gln -92	-	expression tag
Gly -91	-	expression tag
Pro -90	-	expression tag
Asp -89	-	expression tag
Ser -88	-	expression tag
Ala -87	-	expression tag
Thr -86	-	expression tag
His -85	-	expression tag
Ile -84	-	expression tag
Lys -83	-	expression tag
Phe -82	-	expression tag
Ser -81	-	expression tag
Lys -80	-	expression tag
Arg -79	-	expression tag
Asp -78	-	expression tag
Glu -77	-	expression tag
Asp -76	-	expression tag
Gly -75	-	expression tag
Lys -74	-	expression tag
Glu -73	-	expression tag
Leu -72	-	expression tag
Ala -71	-	expression tag
Gly -70	-	expression tag
Ala -69	-	expression tag
Thr -68	-	expression tag
Met -67	-	expression tag
Glu -66	-	expression tag
Leu -65	-	expression tag
Arg -64	-	expression tag
Asp -63	-	expression tag
Ser -62	-	expression tag
Ser -61	-	expression tag
Gly -60	-	expression tag
Lys -59	-	expression tag
Thr -58	-	expression tag
Ile -57	-	expression tag
Ser -56	-	expression tag
Thr -55	-	expression tag
Trp -54	-	expression tag
Ile -53	-	expression tag
Ser -52	-	expression tag
Asp -51	-	expression tag
Gly -50	-	expression tag
Gln -49	-	expression tag
Val -48	-	expression tag
Lys -47	-	expression tag
Asp -46	-	expression tag
Phe -45	-	expression tag
Tyr -44	-	expression tag
Leu -43	-	expression tag
Tyr -42	-	expression tag
Pro -41	-	expression tag
Gly -40	-	expression tag
Lys -39	-	expression tag
Tyr -38	-	expression tag
Thr -37	-	expression tag
Phe -36	-	expression tag
Val -35	-	expression tag
Glu -34	-	expression tag
Thr -33	-	expression tag
Ala -32	-	expression tag
Ala -31	-	expression tag
Pro -30	-	expression tag
Asp -29	-	expression tag
Gly -28	-	expression tag
Tyr -27	-	expression tag
Glu -26	-	expression tag
Val -25	-	expression tag
Ala -24	-	expression tag
Thr -23	-	expression tag
Ala -22	-	expression tag
Ile -21	-	expression tag
Thr -20	-	expression tag
Phe -19	-	expression tag
Thr -18	-	expression tag
Val -17	-	expression tag
Asn -16	-	expression tag
Glu -15	-	expression tag
Gln -14	-	expression tag
Gly -13	-	expression tag
Gln -12	-	expression tag
Val -11	-	expression tag
Thr -10	-	expression tag
Val -9	-	expression tag
Asn -8	-	expression tag
Gly -7	-	expression tag
Ser -6	-	expression tag
Gly -5	-	expression tag
Ser -4	-	expression tag
Gly -3	-	expression tag
Ser -2	-	expression tag
Gly -1	-	expression tag
Ser 0	-	expression tag
Gly 237	Pro 237	conflict
Ser 238	Lys 238	conflict
Trp 240	-	expression tag
Ser 241	-	expression tag
His 242	-	expression tag
Pro 243	-	expression tag
Gln 244	-	expression tag
Phe 245	-	expression tag
Glu 246	-	expression tag
Lys 247	-	expression tag

M: 1 - 854 (UniProt: P35207)

PDB	External Database	Details
Gln 445	Glu 445	conflict
Gly 835	Lys 835	conflict
Ser 836	Glu 836	conflict
Arg 837	-	insertion
Gly 838	-	insertion
Leu 839	-	insertion
Ser 840	Thr 837	conflict
Leu 842	Gln 839	conflict
Asp 844	Glu 841	conflict
Tyr 845	His 842	conflict
Arg 848	Gln 845	conflict
Leu 849	Ile 846	conflict
Ala 850	Lys 847	conflict
Lys 853	Gln 850	conflict
Asp 854	Glu 851	conflict
Thr 855	-	expression tag
Glu 856	-	expression tag
Phe 857	-	expression tag
Ile 858	-	expression tag
Asp 859	-	expression tag
Gln 860	-	expression tag
Asn 861	-	expression tag
His 862	-	expression tag
Asn 863	-	expression tag
Val 864	-	expression tag
Leu 865	-	expression tag
Leu 866	-	expression tag
Lys 867	-	expression tag
Gly 868	-	expression tag
Arg 869	-	expression tag
Val 870	-	expression tag
Ala 871	-	expression tag
Cys 872	-	expression tag
Glu 873	-	expression tag
Ile 874	-	expression tag
Asn 875	-	expression tag
Ser 876	-	expression tag
Gly 877	-	expression tag
Tyr 878	-	expression tag
Glu 879	-	expression tag
Leu 880	-	expression tag
Val 881	-	expression tag
Leu 882	-	expression tag
Thr 883	-	expression tag
Glu 884	-	expression tag
Leu 885	-	expression tag
Ile 886	-	expression tag
Leu 887	-	expression tag
Asp 888	-	expression tag
Asn 889	-	expression tag
Phe 890	-	expression tag
Leu 891	-	expression tag
Gly 892	-	expression tag
Ser 893	-	expression tag
Phe 894	-	expression tag
Glu 895	-	expression tag
Pro 896	-	expression tag
Glu 897	-	expression tag
Glu 898	-	expression tag
Ile 899	-	expression tag
Val 900	-	expression tag
Ala 901	-	expression tag
Leu 902	-	expression tag
Leu 903	-	expression tag
Ser 904	-	expression tag
Val 905	-	expression tag
Phe 906	-	expression tag
Val 907	-	expression tag
Tyr 908	-	expression tag
Glu 909	-	expression tag
Gly 910	-	expression tag
Lys 911	-	expression tag
Thr 912	-	expression tag
Arg 913	-	expression tag
Glu 914	-	expression tag
Glu 915	-	expression tag
Glu 916	-	expression tag
Pro 917	-	expression tag
Pro 918	-	expression tag
Ile 919	-	expression tag
Val 920	-	expression tag
Thr 921	-	expression tag
Pro 922	-	expression tag
Arg 923	-	expression tag
Leu 924	-	expression tag
Ala 925	-	expression tag
Lys 926	-	expression tag
Gly 927	-	expression tag
Lys 928	-	expression tag
Gln 929	-	expression tag
Arg 930	-	expression tag
Ile 931	-	expression tag
Glu 932	-	expression tag
Glu 933	-	expression tag
Ile 934	-	expression tag
Tyr 935	-	expression tag
Lys 936	-	expression tag
Lys 937	-	expression tag
Met 938	-	expression tag
Leu 939	-	expression tag
Cys 940	-	expression tag
Val 941	-	expression tag
Phe 942	-	expression tag
Asn 943	-	expression tag
Thr 944	-	expression tag
His 945	-	expression tag
Gln 946	-	expression tag
Ile 947	-	expression tag
Pro 948	-	expression tag
Leu 949	-	expression tag
Thr 950	-	expression tag
Gln 951	-	expression tag
Asp 952	-	expression tag
Glu 953	-	expression tag
Ala 954	-	expression tag
Glu 955	-	expression tag
Phe 956	-	expression tag
Leu 957	-	expression tag
Asp 958	-	expression tag
Arg 959	-	expression tag
Lys 960	-	expression tag
Arg 961	-	expression tag
Phe 962	-	expression tag
Ala 963	-	expression tag
Met 964	-	expression tag
Met 965	-	expression tag
Asn 966	-	expression tag
Val 967	-	expression tag
Val 968	-	expression tag
Tyr 969	-	expression tag
Glu 970	-	expression tag
Trp 971	-	expression tag
Ala 972	-	expression tag
Arg 973	-	expression tag
Gly 974	-	expression tag
Leu 975	-	expression tag
Ser 976	-	expression tag
Phe 977	-	expression tag
Lys 978	-	expression tag
Glu 979	-	expression tag
Ile 980	-	expression tag
Met 981	-	expression tag
Glu 982	-	expression tag
Met 983	-	expression tag
Ser 984	-	expression tag
Pro 985	-	expression tag
Glu 986	-	expression tag
Ala 987	-	expression tag
Glu 988	-	expression tag
Gly 989	-	expression tag
Thr 990	-	expression tag
Val 991	-	expression tag
Val 992	-	expression tag
Arg 993	-	expression tag
Val 994	-	expression tag
Ile 995	-	expression tag
Thr 996	-	expression tag
Trp 997	-	expression tag
Leu 998	-	expression tag
Asp 999	-	expression tag
Glu 1000	-	expression tag
Ile 1001	-	expression tag
Cys 1002	-	expression tag
Arg 1003	-	expression tag
Glu 1004	-	expression tag
Val 1005	-	expression tag
Lys 1006	-	expression tag
Thr 1007	-	expression tag
Ala 1008	-	expression tag
Ser 1009	-	expression tag
Ile 1010	-	expression tag
Ile 1011	-	expression tag
Ile 1012	-	expression tag
Gly 1013	-	expression tag
Asn 1014	-	expression tag
Ser 1015	-	expression tag
Thr 1016	-	expression tag
Leu 1017	-	expression tag
His 1018	-	expression tag
Met 1019	-	expression tag
Lys 1020	-	expression tag
Met 1021	-	expression tag
Ser 1022	-	expression tag
Arg 1023	-	expression tag
Ala 1024	-	expression tag
Gln 1025	-	expression tag
Glu 1026	-	expression tag
Leu 1027	-	expression tag
Ile 1028	-	expression tag
Lys 1029	-	expression tag
Arg 1030	-	expression tag
Asp 1031	-	expression tag
Ile 1032	-	expression tag
Val 1033	-	expression tag
Phe 1034	-	expression tag
Ala 1035	-	expression tag
Ala 1036	-	expression tag
Ser 1037	-	expression tag
Leu 1038	-	expression tag
Tyr 1039	-	expression tag
Leu 1040	-	expression tag

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	13
Polymers	Total formula weight	581473.9
Non-Polymers*	Number of molecules	1
Non-Polymers*	Total formula weight	507.2
All*	Total formula weight	581981.1

*Water molecules are not included.

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)