8YFQ

Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	DNA-directed RNA polymerase subunit	polymer	1743	194107.4	1	UniProt (C4R4Y0) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb1
2	B	DNA-directed RNA polymerase subunit beta	polymer	1227	139746.1	1	UniProt (C4QZQ7) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb2
3	C	RNA polymerase II third largest subunit B44, part of central core	polymer	304	34216.3	1	UniProt (C4R7L2) Pfam (PF01193) Pfam (PF01000) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb3
4	D	RNA polymerase II subunit B32	polymer	186	20623.0	1	UniProt (C4R2U9) Pfam (PF03874) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb4
5	E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	214	24962.7	1	UniProt (C4R3P8) Pfam (PF03871) Pfam (PF01191) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb5
6	F	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	polymer	155	17803.6	1	UniProt (C4R1V1) Pfam (PF01192) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb6
7	G	RNA polymerase II subunit	polymer	171	18802.6	1	UniProt (C4R9A1) Pfam (PF03876) Pfam (PF00575) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb7
8	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	145	16249.2	1	UniProt (C4R273) Pfam (PF03870) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb8
9	I	DNA-directed RNA polymerase subunit	polymer	115	13612.3	1	UniProt (F2QPE6) Pfam (PF02150) Pfam (PF01096) In PDB	Komagataella phaffii
10	J	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	polymer	72	8554.1	1	UniProt (C4R009) Pfam (PF01194) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb10
11	K	RNA polymerase II subunit B12.5	polymer	118	13832.9	1	UniProt (C4R3Z5) Pfam (PF13656) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb11
12	L	RNA polymerase subunit ABC10-alpha	polymer	72	7862.0	1	UniProt (F2QMI1) Pfam (PF03604) In PDB	Komagataella phaffii	RNA polymerase II subunit Rpb12
13	N	DNA (90-mer)	polymer	90	27700.8	1		synthetic construct
14	T	DNA (90-mer)	polymer	90	27788.8	1		synthetic construct
15	P	RNA (22-mer)	polymer	22	7050.3	1		synthetic construct
16	R	5'-3' exoribonuclease	polymer	1006	115397.6	1	UniProt (F2QV79) Pfam (PF03159) Pfam (PF17846) In PDB	Komagataella phaffii
17	S	Decapping nuclease	polymer	384	44596.0	1	UniProt (F2QLF5) Pfam (PF08652) In PDB	Komagataella phaffii
18	A, B, C, I, J...	ZINC ION	non-polymer		65.4	8	Chemie (ZN)
19	A	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)

Sequence modifications

R: 1 - 994 (UniProt: F2QV79)

PDB	External Database	Details
Gln 203	Glu 203	engineered mutation
Gln 205	Glu 205	engineered mutation
Asn 233	Asp 233	engineered mutation
Asn 235	Asp 235	engineered mutation
Asn 330	Asp 330	engineered mutation
Ser 995	-	expression tag
Gly 996	-	expression tag
Pro 997	-	expression tag
Ser 998	-	expression tag
Ser 999	-	expression tag
Gly 1000	-	expression tag
Leu 1001	-	expression tag
Glu 1002	-	expression tag
Val 1003	-	expression tag
Leu 1004	-	expression tag
Phe 1005	-	expression tag
Gln 1006	-	expression tag

S: 1 - 381 (UniProt: F2QLF5)

PDB	External Database	Details
Gly -2	-	expression tag
Pro -1	-	expression tag
Gly 0	-	expression tag
Ala 213	Glu 213	engineered mutation
Ala 215	Asp 215	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	17
	Total formula weight	732905.6
Non-Polymers*	Number of molecules	9
	Total formula weight	547.6
All*	Total formula weight	733453.2

*Water molecules are not included.