5JEA

Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Exosome complex component RRP45	polymer	305	34001.9	1	UniProt (Q05636) Pfam (PF01138) Pfam (PF03725)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 45
2	B (B)	Exosome complex component SKI6	polymer	249	27892.0	1	UniProt (P46948) Pfam (PF01138) Pfam (PF03725)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Extracellular mutant protein 20,Ribosomal RNA-processing protein 41,Superkiller protein 6
3	C (C)	Exosome complex component RRP43	polymer	394	44109.0	1	UniProt (P25359) Pfam (PF01138)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 43
4	D (D)	Exosome complex component RRP46	polymer	226	24659.4	1	UniProt (P53256) Pfam (PF01138) Pfam (PF03725)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 46
5	E (E)	Exosome complex component RRP42	polymer	268	29391.5	1	UniProt (Q12277)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 42
6	F (F)	Exosome complex component MTR3	polymer	250	27573.9	1	UniProt (P48240) Pfam (PF01138)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	mRNA transport regulator 3
7	G (G)	Exosome complex component RRP40	polymer	244	26939.7	1	UniProt (Q08285) Pfam (PF21262) Pfam (PF15985) Pfam (PF18311)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Ribosomal RNA-processing protein 40
8	H (H)	Exosome complex component RRP4	polymer	316	34603.1	1	UniProt (P38792) Pfam (PF14382) Pfam (PF21266) Pfam (PF15985)	Saccharomyces cerevisiae (Baker's yeast)	Ribosomal RNA-processing protein 4
9	I (I)	Exosome complex component CSL4	polymer	295	31911.6	1	UniProt (P53859) Pfam (PF21551) Pfam (PF10447)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	CEP1 synthetic lethal protein 4
10	J (J)	Exosome complex exonuclease DIS3	polymer	1005	114212.1	1	UniProt (Q08162) Pfam (PF13638) Pfam (PF17216) Pfam (PF17849) Pfam (PF00773) Pfam (PF17215)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Chromosome disjunction protein 3,Ribosomal RNA-processing protein 44
11	K (K)	Superkiller protein 7,Endolysin	polymer	279	31666.1	1	UniProt (Q08491) UniProt (P00720) Pfam (PF00959)	Saccharomyces cerevisiae (Baker's yeast)	Lysis protein,Lysozyme,Muramidase
12	L (R)	RNA (29-MER)	polymer	46	14336.1	1		synthetic construct
13	M, N, Q, R, T... (A, C, D, G, J)	(4S)-2-METHYL-2,4-PENTANEDIOL	non-polymer		118.2	7	Chemie (MPD)
14	O, P, S, X (B, F, J)	SODIUM ION	non-polymer		23.0	4	Chemie (NA)
15	W (J)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)
16	AA, BA, CA, DA, EA... (C, D, E, F, G...)	water	water		18.0	134	Chemie (HOH)

Sequence modifications

B: 1 - 246 (UniProt: P46948)

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

E: 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

F: 1 - 250 (UniProt: P48240)

PDB	External Database	Details
Thr 161	Met 161	conflict

G: 1 - 240 (UniProt: Q08285)

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

H: 50 - 359 (UniProt: P38792)

PDB	External Database	Details
Thr 44	-	expression tag
Gly 45	-	expression tag
Gly 46	-	expression tag
Arg 47	-	expression tag
Ser 48	-	expression tag
Met 49	-	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 -3	-	expression tag
Pro -2	-	expression tag
Asp -1	-	expression tag
Ser 0	-	expression tag
Asn 171	Asp 171	conflict
Asn 551	Asp 551	conflict

K: 116 - 225 (UniProt: Q08491)

PDB	External Database	Details
Gly 111	-	expression tag
Pro 112	-	expression tag
Asp 113	-	expression tag
Ser 114	-	expression tag
Met 115	-	expression tag

K: 226 - 389 (UniProt: P00720)

PDB	External Database	Details
Gly 237	Arg 12	conflict
Thr 279	Cys 54	conflict
Ala 322	Cys 97	conflict
Arg 362	Ile 137	conflict
His 364	Tyr 139	conflict

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	441296.5
Non-Polymers*	Number of molecules	12
	Total formula weight	984.6
All*	Total formula weight	442281.1

*Water molecules are not included.