8JCH

Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1)

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 II subunit RPB1	polymer	1733	191821.6	1	UniProt (P04050) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit 1,RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220
2	B	DNA-directed RNA polymerase II subunit RPB2	polymer	1259	143336.8	1	UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
3	C	DNA-directed RNA polymerase II subunit RPB3	polymer	318	35330.5	1	UniProt (P16370) Pfam (PF01193) Pfam (PF01000) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit 3,RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
4	D	DNA-directed RNA polymerase II subunit RPB4	polymer	221	25451.2	1	UniProt (P20433) Pfam (PF03874) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
5	E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	215	25117.1	1	UniProt (P20434) Pfam (PF03871) Pfam (PF01191) In PDB	Saccharomyces cerevisiae S288C	RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
6	F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	polymer	155	17931.8	1	UniProt (P20435) Pfam (PF01192) In PDB	Saccharomyces cerevisiae S288C	RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
7	G	DNA-directed RNA polymerase II subunit RPB7	polymer	171	19081.1	1	UniProt (P34087) Pfam (PF03876) Pfam (PF00575) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit B7,B16
8	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	146	16525.4	1	UniProt (P20436) Pfam (PF03870) In PDB	Saccharomyces cerevisiae S288C	RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
9	I	DNA-directed RNA polymerase II subunit RPB9	polymer	122	14308.2	1	UniProt (P27999) Pfam (PF02150) Pfam (PF01096) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9
10	J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	polymer	70	8290.7	1	UniProt (P22139) Pfam (PF01194) In PDB	Saccharomyces cerevisiae S288C	RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
11	K	DNA-directed RNA polymerase II subunit RPB11	polymer	120	13633.5	1	UniProt (P38902) Pfam (PF13656) In PDB	Saccharomyces cerevisiae S288C	RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide
12	L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	polymer	70	7730.0	1	UniProt (P40422) Pfam (PF03604) In PDB	Saccharomyces cerevisiae S288C	RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
13	M	5'-3' exoribonuclease 2	polymer	1019	117606.5	1	UniProt (Q02792) Pfam (PF03159) Pfam (PF17846) In PDB	Saccharomyces cerevisiae S288C	Ribonucleic acid-trafficking protein 1,p116
14	N	DNA (38-MER)	polymer	48	14892.5	1		synthetic construct
15	O	Decapping nuclease RAI1	polymer	387	44571.4	1	UniProt (P53063) Pfam (PF08652) In PDB	Saccharomyces cerevisiae S288C	ScRai1,NAD-capped RNA hydrolase RAI1,DeNADding enzyme RAI1,RAT1-interacting protein
16	P	RNA	polymer	23	7403.5	1		synthetic construct
17	T	DNA (38-MER)	polymer	48	14658.4	1		synthetic construct
18	W	Transcription elongation factor SPT5	polymer	1063	115798.0	1	UniProt (P27692) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) Pfam (PF12815) In PDB	Saccharomyces cerevisiae S288C	Chromatin elongation factor SPT5
19	L, A, B, C, I...	ZINC ION	non-polymer		65.4	8	Chemie (ZN)
20	M, O, A	MAGNESIUM ION	non-polymer		24.3	3	Chemie (MG)

Sequence modifications

B: 1 - 1224 (UniProt: P08518)

PDB	External Database	Details
Glu 1225	-	expression tag
Asn 1226	-	expression tag
Leu 1227	-	expression tag
Tyr 1228	-	expression tag
Phe 1229	-	expression tag
Gln 1230	-	expression tag
Gly 1231	-	expression tag
His 1232	-	expression tag
His 1233	-	expression tag
His 1234	-	expression tag
His 1235	-	expression tag
His 1236	-	expression tag
His 1237	-	expression tag
Asp 1238	-	expression tag
Tyr 1239	-	expression tag
Lys 1240	-	expression tag
Asp 1241	-	expression tag
His 1242	-	expression tag
Asp 1243	-	expression tag
Gly 1244	-	expression tag
Asp 1245	-	expression tag
Tyr 1246	-	expression tag
Lys 1247	-	expression tag
Asp 1248	-	expression tag
His 1249	-	expression tag
Asp 1250	-	expression tag
Ile 1251	-	expression tag
Asp 1252	-	expression tag
Tyr 1253	-	expression tag
Lys 1254	-	expression tag
Asp 1255	-	expression tag
Asp 1256	-	expression tag
Asp 1257	-	expression tag
Asp 1258	-	expression tag
Lys 1259	-	expression tag

M: 1 - 1006 (UniProt: Q02792)

PDB	External Database	Details
Met -12	-	initiating methionine
Gly -11	-	expression tag
Ser -10	-	expression tag
Ser -9	-	expression tag
His -8	-	expression tag
His -7	-	expression tag
His -6	-	expression tag
His -5	-	expression tag
His -4	-	expression tag
His -3	-	expression tag
Ser -2	-	expression tag
Gln -1	-	expression tag
Asp 0	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	18
	Total formula weight	833488.0
Non-Polymers*	Number of molecules	11
	Total formula weight	596.2
All*	Total formula weight	834084.2

*Water molecules are not included.