5GMK

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Pre-mRNA-splicing factor 8	polymer	2413	279867.5	1	UniProt (P33334) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF08084) In PDB	Saccharomyces cerevisiae S288C
2	C	Pre-mRNA-splicing factor SNU114	polymer	1008	114174.0	1	UniProt (P36048) Pfam (PF03764) Pfam (PF00679) Pfam (PF16004) Pfam (PF00009) In PDB	Saccharomyces cerevisiae S288C	114 kDa U5 small nuclear ribonucleoprotein component
3	D	U5 snRNA	polymer	214	68643.3	1		Saccharomyces cerevisiae S288c
4	E	U6 snRNA	polymer	112	35883.2	1		Saccharomyces cerevisiae S288c
5	L	U2 snRNA	polymer	1175	376267.4	1		Saccharomyces cerevisiae S288c
6	M	Intron_BPS	polymer	29	9161.4	1		Saccharomyces cerevisiae S288c
7	B	5'-Exon	polymer	13	4112.5	1		Saccharomyces cerevisiae S288c
8	N	5'-Splicing Site	polymer	15	4694.7	1		Saccharomyces cerevisiae S288c
9	J	Pre-mRNA-splicing factor CWC21	polymer	135	15793.6	1	UniProt (Q03375) Pfam (PF08312) In PDB	Saccharomyces cerevisiae S288C	Complexed with CEF1 protein 21
10	O	Pre-mRNA-splicing factor PRP46	polymer	451	50771.3	1	UniProt (Q12417) Pfam (PF00400) In PDB	Saccharomyces cerevisiae S288C	Pre-mRNA-processing protein 46
11	P	Pre-mRNA-processing protein 45	polymer	379	42548.7	1	UniProt (P28004) Pfam (PF02731) In PDB	Saccharomyces cerevisiae S288C
12	Q	Pre-mRNA-splicing factor SLT11	polymer	364	40988.6	1	UniProt (P38241) Pfam (PF21369) In PDB	Saccharomyces cerevisiae S288C	Synthetic lethality with U2 protein 11
13	R	Pre-mRNA-splicing factor CWC2	polymer	339	38486.6	1	UniProt (Q12046) Pfam (PF16131) Pfam (PF00076) In PDB	Saccharomyces cerevisiae S288C	Complexed with CEF1 protein 2
14	S	Pre-mRNA-splicing factor CWC15	polymer	175	19975.2	1	UniProt (Q03772) Pfam (PF04889) In PDB	Saccharomyces cerevisiae S288C	Complexed with CEF1 protein 15
15	T	Pre-mRNA-splicing factor BUD31	polymer	157	18484.5	1	UniProt (P25337) Pfam (PF01125) In PDB	Saccharomyces cerevisiae S288C	Bud site selection protein 31,Complexed with CEF1 protein 14
16	Z	Pre-mRNA-splicing factor CWC22	polymer	577	67386.1	1	UniProt (P53333) Pfam (PF02847) In PDB	Saccharomyces cerevisiae S288C	Complexed with CEF1 protein 22
17	c	Pre-mRNA-splicing factor CEF1	polymer	587	61057.6	1	UniProt (Q03654) Pfam (PF00249) Pfam (PF11831) In PDB	Saccharomyces cerevisiae S288C
18	d	Pre-mRNA-splicing factor CLF1	polymer	687	68044.6	1	UniProt (Q12309) In PDB	Saccharomyces cerevisiae S288C	Crooked neck-like factor 1
19	F	Protein CWC16	polymer	278	32371.1	1	UniProt (P28320) Pfam (PF04502) In PDB	Saccharomyces cerevisiae S288C
20	G	Pre-mRNA-splicing factor CWC25	polymer	179	20412.5	1	UniProt (P53854) Pfam (PF10197) Pfam (PF12542) In PDB	Saccharomyces cerevisiae S288C	Complexed with CEF1 protein 25
21	H	Pre-mRNA-splicing factor ISY1	polymer	235	28073.8	1	UniProt (P21374) Pfam (PF06246) In PDB	Saccharomyces cerevisiae S288C	Interactor of SYF1
22	I	Pre-mRNA-splicing factor SYF2	polymer	215	24850.7	1	UniProt (P53277) Pfam (PF08231) In PDB	Saccharomyces cerevisiae S288C	Synthetic lethal with CDC40 protein 2
23	v	Pre-mRNA-splicing factor SYF1	polymer	859	78125.6	1	UniProt (Q04048) In PDB	Saccharomyces cerevisiae S288c	Synthetic lethal with CDC40 protein 1
24	n	Pre-mRNA-processing factor 17	polymer	455	52128.8	1	UniProt (P40968) Pfam (PF00400) In PDB	Saccharomyces cerevisiae S288C
25	o, p, q, r	Pre-mRNA-processing factor 19	polymer	503	56629.8	4	UniProt (P32523) Pfam (PF08606) In PDB	Saccharomyces cerevisiae S288C
26	t	Pre-mRNA-splicing factor SNT309	polymer	175	20741.5	1	UniProt (Q06091) In PDB	Saccharomyces cerevisiae S288C	Synergistic to PRP19 mutation protein 309
27	k, s	Small nuclear ribonucleoprotein-associated protein B	polymer	196	22427.0	2	UniProt (P40018) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	snRNP-B,Sm protein B,SmB
28	i, u	Small nuclear ribonucleoprotein E	polymer	94	10385.1	2	UniProt (Q12330) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	snRNP-E,Sm protein E,SmE
29	h, w	Small nuclear ribonucleoprotein F	polymer	86	9669.9	2	UniProt (P54999) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	snRNP-F,Sm protein F,SmF
30	j, x	Small nuclear ribonucleoprotein G	polymer	77	8490.8	2	UniProt (P40204) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	snRNP-G,Sm protein G,SmG
31	l, y	Small nuclear ribonucleoprotein Sm D3	polymer	101	11240.1	2	UniProt (P43321) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	Sm-D3,snRNP core protein D3
32	m, z	Small nuclear ribonucleoprotein Sm D1	polymer	146	16296.8	2	UniProt (Q02260) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	Sm-D1,snRNP core protein D1
33	g, e	Small nuclear ribonucleoprotein Sm D2	polymer	110	12876.1	2	UniProt (Q06217) Pfam (PF01423) In PDB	Saccharomyces cerevisiae S288C	Sm-D2,snRNP core protein D2
34	a	U2 small nuclear ribonucleoprotein B''	polymer	111	12850.9	1	UniProt (P40567) Pfam (PF13893) In PDB	Saccharomyces cerevisiae S288C	U2 snRNP B''
35	b	U2 small nuclear ribonucleoprotein A'	polymer	238	27232.3	1	UniProt (Q08963) Pfam (PF14580) In PDB	Saccharomyces cerevisiae S288C	U2 snRNP A',Looks exceptionally like U2A protein 1
36	C	GUANOSINE-5'-TRIPHOSPHATE	non-polymer		523.2	1	Chemie (GTP)
37	C, E	MAGNESIUM ION	non-polymer		24.3	6	Chemie (MG)
38	Q, R, T, F	ZINC ION	non-polymer		65.4	7	Chemie (ZN)

Sequence modifications

c: 1 - 253 (UniProt: Q03654)
c: 253 - 469 (PDB: 5GMK)
c: 482 - 587 (UniProt: Q03654)
d: 1 - 275 (UniProt: Q12309)
d: 295 - 744 (PDB: 5GMK)
v: -39 - 561 (PDB: 5GMK)
v: 569 - 734 (UniProt: Q04048)
v: 740 - 867 (PDB: 5GMK)

Contents of the asymmetric unit

Polymers	Number of chains	45
	Total formula weight	2022418.6
Non-Polymers*	Number of molecules	14
	Total formula weight	1126.9
All*	Total formula weight	2023545.5

*Water molecules are not included.