7NKX

RNA polymerase II-Spt4/5-nucleosome-Chd1 structure

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (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 (Baker's yeast)	RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220
2	B (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 (Baker's yeast)	RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
3	C (C)	DNA-directed RNA polymerase II subunit RPB3	polymer	318	35330.5	1	UniProt (P16370) Pfam (PF01193) Pfam (PF01000)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
4	D (E)	DNA-directed RNA polymerases I, II, and III subunit RPABC1	polymer	215	25117.1	1	UniProt (P20434) Pfam (PF03871) Pfam (PF01191)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
5	E (F)	DNA-directed RNA polymerases I, II, and III subunit RPABC2	polymer	155	17931.8	1	UniProt (P20435) Pfam (PF01192)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
6	F (H)	DNA-directed RNA polymerases I, II, and III subunit RPABC3	polymer	146	16525.4	1	UniProt (P20436) Pfam (PF03870)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
7	G (I)	DNA-directed RNA polymerase II subunit RPB9	polymer	122	14308.2	1	UniProt (P27999) Pfam (PF02150) Pfam (PF01096)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9
8	H (J)	DNA-directed RNA polymerases I, II, and III subunit RPABC5	polymer	70	8290.7	1	UniProt (P22139) Pfam (PF01194)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
9	I (K)	DNA-directed RNA polymerase II subunit RPB11	polymer	120	13633.5	1	UniProt (P38902) Pfam (PF13656)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide
10	J (L)	DNA-directed RNA polymerases I, II, and III subunit RPABC4	polymer	70	7730.0	1	UniProt (P40422) Pfam (PF03604)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
11	K, O (a, e)	Histone H3.2	polymer	136	15435.1	2	UniProt (P84233) Pfam (PF00125)	Xenopus laevis (African clawed frog)
12	L, P (b, f)	Histone H4	polymer	103	11394.4	2	UniProt (P62799) Pfam (PF15511)	Xenopus laevis (African clawed frog)
13	M, Q (c, g)	Histone H2A type 1	polymer	130	14109.4	2	UniProt (P06897) Pfam (PF00125) Pfam (PF16211)	Xenopus laevis (African clawed frog)
14	N, R (d, h)	Histone H2B 1.1	polymer	123	13655.9	2	UniProt (P02281) Pfam (PF00125)	Xenopus laevis (African clawed frog)	H2B1.1
15	S (T)	DNA (139-MER)	polymer	185	56835.3	1		synthetic construct
16	T (N)	DNA (128-MER)	polymer	176	54656.7	1		synthetic construct
17	U (W)	Chromo domain-containing protein 1	polymer	1468	168496.6	1	UniProt (P32657) Pfam (PF00385) Pfam (PF00176) Pfam (PF00271) Pfam (PF18196) Pfam (PF13907)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	ATP-dependent helicase CHD1
18	V (P)	RNA	polymer	69	21902.6	1		synthetic construct
19	W (Y)	Chromatin elongation factor SPT4	polymer	102	11168.8	1	UniProt (A0A6A5PX04) Pfam (PF06093) UniProt (by SIFTS) (P32914)	Saccharomyces cerevisiae (Baker's yeast)	Transcription elongation factor SPT4
20	X (Z)	Transcription elongation factor SPT5	polymer	1066	116096.2	1	UniProt (P27692) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) Pfam (PF12815)	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	Chromatin elongation factor SPT5
21	Y (D)	DNA-directed RNA polymerase II subunit RPB4	polymer	221	25451.2	1	UniProt (P20433) Pfam (PF03874)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
22	Z (G)	DNA-directed RNA polymerase II subunit RPB7	polymer	171	19081.1	1	UniProt (P34087) Pfam (PF03876) Pfam (PF00575)	Saccharomyces cerevisiae (Baker's yeast)	RNA polymerase II subunit B7,B16
23	AA, BA, DA, EA, FA... (A, B, C, I, J...)	ZINC ION	non-polymer		65.4	8	Chemie (ZN)
24	CA (A)	MAGNESIUM ION	non-polymer		24.3	1	Chemie (MG)
25	JA (W)	ADENOSINE-5'-DIPHOSPHATE	non-polymer		427.2	1	Chemie (ADP)
26	KA (W)	BERYLLIUM TRIFLUORIDE ION	non-polymer		66.0	1	Chemie (BEF)

Sequence modifications

a, e: 0 - 135 (UniProt: P84233)

PDB	External Database	Details
Ala 102	Gly 103	conflict

c, g: 0 - 129 (UniProt: P06897)

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

d, h: 1 - 122 (UniProt: P02281)

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

Z: 1 - 1063 (UniProt: P27692)

PDB	External Database	Details
Ser -2	-	expression tag
Asn -1	-	expression tag
Ala 0	-	expression tag
Leu 376	Lys 376	conflict
Glu 377	Ser 377	conflict

Contents of the asymmetric unit

Polymers	Number of chains	26
	Total formula weight	1052504.4
Non-Polymers*	Number of molecules	11
	Total formula weight	1040.8
All*	Total formula weight	1053545.1

*Water molecules are not included.