5C0W

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Exosome complex component RRP45	polymer	305	34001.9	1	UniProt (Q05636) Pfam (PF01138) Pfam (PF03725) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 45
2	B	Exosome complex component SKI6	polymer	248	27794.9	1	UniProt (P46948) Pfam (PF01138) Pfam (PF03725) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Extracellular mutant protein 20,Ribosomal RNA-processing protein 41,Superkiller protein 6
3	C	Exosome complex component RRP43	polymer	394	44109.0	1	UniProt (P25359) Pfam (PF01138) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 43
4	D	Exosome complex component RRP46	polymer	245	26914.0	1	UniProt (P53256) Pfam (PF01138) Pfam (PF03725) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 46
5	E	Exosome complex component RRP42	polymer	267	29294.4	1	UniProt (Q12277) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 42
6	F	Exosome complex component MTR3	polymer	250	27559.9	1	UniProt (P48240) Pfam (PF01138) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	mRNA transport regulator 3
7	G	Exosome complex component RRP40	polymer	243	26875.7	1	UniProt (Q08285) Pfam (PF21262) Pfam (PF15985) Pfam (PF18311) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 40
8	H	Exosome complex component RRP4	polymer	361	39714.4	1	UniProt (P38792) Pfam (PF14382) Pfam (PF21266) Pfam (PF15985) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 4
9	I	Exosome complex component CSL4	polymer	295	31911.6	1	UniProt (P53859) Pfam (PF21551) Pfam (PF10447) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	CEP1 synthetic lethal protein 4
10	J	Exosome complex exonuclease DIS3	polymer	1004	114081.0	1	UniProt (Q08162) Pfam (PF13638) Pfam (PF17216) Pfam (PF17849) Pfam (PF00773) Pfam (PF17215) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Chromosome disjunction protein 3,Ribosomal RNA-processing protein 44
11	K	Exosome complex exonuclease RRP6	polymer	695	79649.4	1	UniProt (Q12149) Pfam (PF08066) Pfam (PF01612) Pfam (PF00570) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 6
12	L	Exosome complex protein LRP1	polymer	184	21086.3	1	UniProt (P38801) Pfam (PF04000) In PDB	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Like an rRNA processing protein 1,Yeast C1D domain-containing protein,rRNA processing protein 47
13	R, N	RNA synthetic	polymer	18	5811.6	2		synthetic construct
14	J	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)
15	J	ZINC ION	non-polymer		65.4	1	Chemie (ZN)

Sequence modifications

B: 1 - 246 (UniProt: P46948)

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

C: 1 - 394 (UniProt: P25359)

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

D: 1 - 223 (UniProt: P53256)

PDB	External Database	Details
Gly -21	-	expression tag
His -20	-	expression tag
Gly -19	-	expression tag
Asn -18	-	expression tag
Asn -17	-	expression tag
Lys -16	-	expression tag
Glu -15	-	expression tag
Pro -14	-	expression tag
Asn -13	-	expression tag
Thr -12	-	expression tag
Lys -11	-	expression tag
Asn -10	-	expression tag
Arg -9	-	expression tag
Leu -8	-	expression tag
Asp -7	-	expression tag
Ser -6	-	expression tag
Ala -5	-	expression tag
Glu -4	-	expression tag
Lys -3	-	expression tag
Lys -2	-	expression tag
Lys -1	-	expression tag
Lys 0	-	expression tag

E: 1 - 265 (UniProt: Q12277)

PDB	External Database	Details
Gly -1	-	expression tag
His 0	-	expression tag
Ile 138	Val 138	engineered mutation

F: 1 - 250 (UniProt: P48240)

PDB	External Database	Details
Ser 75	Thr 75	engineered mutation
Thr 161	Met 161	engineered mutation

G: 1 - 240 (UniProt: Q08285)

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

H: 1 - 359 (UniProt: P38792)

PDB	External Database	Details
Arg -1	-	expression tag
Ser 0	-	expression tag

I: 1 - 292 (UniProt: P53859)

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

J: 1 - 1001 (UniProt: Q08162)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Ala 0	-	expression tag
Asn 171	Asp 171	engineered mutation
Asn 551	Asp 551	engineered mutation

K: 1 - 693 (UniProt: Q12149)

PDB	External Database	Details
Gly -1	-	expression tag
Ala 0	-	expression tag
Ala 2	Thr 2	engineered mutation
Asn 296	Asp 296	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	14
	Total formula weight	514615.7
Non-Polymers*	Number of molecules	2
	Total formula weight	89.7
All*	Total formula weight	514705.5

*Water molecules are not included.