6I84

Structure of transcribing RNA polymerase II-nucleosome complex

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, H (M, S)	Histone H3.2	polymer	136	15435.1	2	UniProt (P84233) Pfam (PF00125)	Xenopus laevis (African clawed frog)
2	B, C (Q, V)	Histone H2A type 1	polymer	130	14109.4	2	UniProt (P06897) Pfam (PF00125) Pfam (PF16211)	Xenopus laevis (African clawed frog)
3	D (T)	DNA (170-MER)	polymer	169	52041.2	1		synthetic construct
4	E (N)	DNA (158-MER)	polymer	160	49537.6	1		synthetic construct
5	F, I (O, U)	Histone H4	polymer	103	11394.4	2	UniProt (P62799) Pfam (PF15511)	Xenopus laevis (African clawed frog)
6	G, J (R, W)	Histone H2B 1.1	polymer	123	13655.9	2	UniProt (P02281) Pfam (PF00125)	Xenopus laevis (African clawed frog)	H2B1.1
7	K (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)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220
8	L (B)	DNA-directed RNA polymerase II subunit RPB2	polymer	1224	138937.3	1	UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
9	M (C)	DNA-directed RNA polymerase II subunit RPB3	polymer	348	38809.1	1	UniProt (P16370) Pfam (PF01193) Pfam (PF01000)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
10	N (D)	DNA-directed RNA polymerase II subunit RPB4	polymer	221	25451.2	1	UniProt (P20433) Pfam (PF03874)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
11	O (E)	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	215	25117.1	1	UniProt (P20434) Pfam (PF03871) Pfam (PF01191)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
12	P (F)	DNA-directed RNA polymerases I, II, and III subunit RPABC2	polymer	155	17931.8	1	UniProt (P20435) Pfam (PF01192)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
13	Q (G)	DNA-directed RNA polymerase II subunit RPB7	polymer	171	19081.1	1	UniProt (P34087) Pfam (PF03876) Pfam (PF00575)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B7,B16
14	R (H)	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	146	16525.4	1	UniProt (P20436) Pfam (PF03870)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
15	S (I)	DNA-directed RNA polymerase II subunit RPB9	polymer	122	14308.2	1	UniProt (P27999) Pfam (PF02150) Pfam (PF01096)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9
16	T (J)	DNA-directed RNA polymerases I, II, and III subunit RPABC5	polymer	70	8290.7	1	UniProt (P22139) Pfam (PF01194)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
17	U (K)	DNA-directed RNA polymerase II subunit RPB11	polymer	120	13633.5	1	UniProt (P38902) Pfam (PF13656)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide
18	V (L)	DNA-directed RNA polymerases I, II, and III subunit RPABC4	polymer	70	7730.0	1	UniProt (P40422) Pfam (PF03604)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
19	W (P)	RNA	polymer	10	3137.9	1		synthetic construct
20	AA, BA, CA, DA, EA... (B, C, I, J, L...)	ZINC ION	non-polymer		65.4	8	Chemie (ZN)
21	Z (A)	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)

Sequence modifications

M, S: 0 - 135 (UniProt: P84233)

PDB	External Database	Details
Ala 102	Gly 103	conflict

Q, V: 0 - 129 (UniProt: P06897)

PDB	External Database	Details
Arg 99	Gly 100	conflict
Ser 123	Ala 124	conflict

R, W: 1 - 122 (UniProt: P02281)

PDB	External Database	Details
Met 0	-	initiating methionine
Thr 29	Ser 33	conflict

C: 1 - 318 (UniProt: P16370)

PDB	External Database	Details
Met -29	-	initiating methionine
Gly -28	-	expression tag
Ser -27	-	expression tag
His -26	-	expression tag
His -25	-	expression tag
His -24	-	expression tag
His -23	-	expression tag
His -22	-	expression tag
His -21	-	expression tag
Ser -20	-	expression tag
Asn -19	-	expression tag
Ser -18	-	expression tag
Gly -17	-	expression tag
Leu -16	-	expression tag
Asn -15	-	expression tag
Asp -14	-	expression tag
Ile -13	-	expression tag
Phe -12	-	expression tag
Glu -11	-	expression tag
Ala -10	-	expression tag
Gln -9	-	expression tag
Lys -8	-	expression tag
Ile -7	-	expression tag
Glu -6	-	expression tag
Trp -5	-	expression tag
His -4	-	expression tag
Glu -3	-	expression tag
Asp -2	-	expression tag
Thr -1	-	expression tag
Gly 0	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	23
	Total formula weight	731543.4
Non-Polymers*	Number of molecules	9
	Total formula weight	547.6
All*	Total formula weight	732091.0

*Water molecules are not included.