7B7U

Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2

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	1970	217450.1	1	UniProt (I3LJR4) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) In PDB	Sus scrofa domesticus (domestic pig)
2	B	DNA-directed RNA polymerase subunit beta	polymer	1174	134041.4	1	UniProt (A0A0B8RVL1) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) UniProt (by SIFTS) (I3LGP4) In PDB	Sus scrofa domesticus (domestic pig)
3	C	DNA-directed RNA polymerase II subunit RPB3	polymer	271	30997.6	1	UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) In PDB	Sus scrofa domesticus (domestic pig)	RNA polymerase II subunit C
4	E	DNA-directed RNA polymerase II subunit E	polymer	210	24644.3	1	UniProt (I3LSI7) Pfam (PF03871) Pfam (PF01191) In PDB	Sus scrofa domesticus (domestic pig)	RPB5 homolog
5	F	DNA-directed RNA polymerase II subunit F	polymer	127	14477.0	1	UniProt (F1SKN8) Pfam (PF01192) UniProt (by SIFTS) (A0A4X1VEK9) In PDB	Sus scrofa domesticus (domestic pig)	DNA-directed RNA polymerases I,II,and III subunit RPABC2,RPB6 homolog
6	H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	150	17162.3	1	UniProt (A0A4X1ULF2) Pfam (PF03870) UniProt (by SIFTS) (I3LCB2) In PDB	Sus scrofa domesticus (domestic pig)
7	I	DNA-directed RNA polymerase II subunit RPB9	polymer	125	14541.2	1	UniProt (P60899) Pfam (PF02150) Pfam (PF01096) In PDB	Sus scrofa domesticus (domestic pig)	RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5
8	J	Uncharacterized Protein	polymer	67	7655.1	1	Pfam (PF01194) UniProt (by SIFTS) (A0A4X1VYD0) In PDB	Sus scrofa domesticus (domestic pig)
9	K	RNA_pol_L_2 domain-containing protein	polymer	117	13310.3	1	UniProt (A0A4X1UK25) Pfam (PF13656) UniProt (by SIFTS) (F1RKE4) In PDB	Sus scrofa domesticus (domestic pig)
10	L	RNA polymerase II subunit K	polymer	58	7018.2	1	UniProt (I3LN51) Pfam (PF03604) UniProt (by SIFTS) (A0A4X1TRS6) In PDB	Sus scrofa domesticus (domestic pig)
11	M	Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2	polymer	612	69614.8	1	UniProt (Q8IXW5) Pfam (PF04181) In PDB	Homo sapiens (Human)	RNA polymerase II-associated protein 2
12	N	Unknown	polymer	30	2571.2	1		Homo sapiens (Human)
13	C, I, J, L, M	ZINC ION	non-polymer		65.4	6	Chemie (ZN)

Sequence modifications

A: 1 - 1970 (UniProt: I3LJR4)

PDB	External Database	Details
Ser 487	-	insertion
Val 488	Arg 487	conflict
Thr 489	Ser 488	conflict
Thr 490	Val 489	conflict
Pro 491	His 490	conflict
Tyr 492	Trp 491	conflict
Asn 493	Leu 492	conflict
Ala 494	Arg 493	conflict
Asp 495	Glu 494	conflict
Phe 496	Ala 495	conflict
Asp 497	Ala 496	conflict
Asp 499	-	insertion
Glu 500	-	insertion
Met 501	Ala 498	conflict
Asn 502	Gly 499	conflict
His 504	-	insertion
Gln 507	-	insertion
Ser 508	-	insertion
Leu 509	Gly 503	conflict
Glu 510	Asp 504	conflict
Arg 512	-	insertion
Ala 513	-	insertion
Glu 514	-	insertion
Ile 515	-	insertion
Gln 516	-	insertion
Glu 517	-	insertion
Leu 518	-	insertion
Ala 519	-	insertion
Met 520	-	insertion
Val 521	-	insertion
Pro 522	-	insertion
Arg 523	-	insertion
Met 524	-	insertion
Ile 525	Gly 506	conflict
Val 526	Gly 507	conflict
Thr 527	Asp 508	conflict
Gln 529	Gly 510	conflict
Ile 1301	-	insertion
Glu 1302	-	insertion
Gln 1303	-	insertion
Ile 1304	-	insertion
Lys 1306	-	insertion
Val 1307	-	insertion
Tyr 1308	-	insertion
Met 1309	-	insertion
His 1310	-	insertion
Leu 1311	Ser 1283	conflict
Pro 1312	Arg 1284	conflict
Gln 1313	Ser 1285	conflict

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	553483.5
Non-Polymers*	Number of molecules	6
	Total formula weight	392.5
All*	Total formula weight	553875.9

*Water molecules are not included.