SMTL ID : 8jh2.1

RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77, C:H.80 ZN.2: 4 residues within 4Å: Chain C: C.107, N.109, C.110, C.168 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.107, C:C.110, C:C.168 ZN.4: 4 residues within 4Å: Chain D: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:C.1182, D:C.1185 ZN.5: 5 residues within 4Å: Chain E: C.85, C.87, C.91, E.93, C.94 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.85, E:C.91, E:C.94 ZN.6: 5 residues within 4Å: Chain K: C.75, C.78, C.103, N.105, C.106 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.78, K:C.103 ZN.7: 3 residues within 4Å: Chain K: C.10, C.29, C.32 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.10, K:C.29, K:C.32 ZN.8: 4 residues within 4Å: Chain L: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.44, L:C.45 ZN.9: 4 residues within 4Å: Chain N: C.33, C.36, C.50, C.53 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.33, N:C.36, N:C.50, N:C.53 ZN.10: 4 residues within 4Å: Chain O: C.25, C.28, C.49, C.52 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.25, O:C.28, O:C.49, O:C.52 ZN.11: 4 residues within 4Å: Chain S: C.12, C.15, C.29, C.32 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.12, S:C.15, S:C.29, S:C.32

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain C: D.482, D.484, D.486 Chain Q: G.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.482, C:D.482, C:D.484, C:D.486

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akatsu, M. et al., Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem. (2023)

Release Date

2023-11-29

Peptides

DNA-directed RNA polymerase subunit: C
DNA-directed RNA polymerase subunit beta: D
RNA polymerase II third largest subunit B44, part of central core: E
RNA polymerase II subunit B32: F
RNA polymerase subunit ABC27: G
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III: H
RNA polymerase II subunit: I
DNA-directed RNA polymerases I, II, and III subunit RPABC3: J
DNA-directed RNA polymerase subunit: K
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III: L
RNA polymerase II subunit B12.5: M
RNA polymerase subunit ABC10-alpha: N
Transcription elongation factor 1 homolog: O
Transcription elongation factor SPT4: S
Transcription elongation factor SPT5: T
Histone H3.3: UY
Histone H4: VZ
Histone H2A type 1-B/E: W0
Histone H2B type 1-J: X1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

O
M

S
V

T
W

U
a

Y
e

V
b

Z
f

W
c

0
g

X
d

1
h

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

RNA polymerase II third largest subunit B44, part of central core

RNA polymerase II subunit B32

RNA polymerase subunit ABC27

RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

RNA polymerase II subunit

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase subunit

RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III

RNA polymerase II subunit B12.5

RNA polymerase subunit ABC10-alpha

Transcription elongation factor 1 homolog

Transcription elongation factor SPT4

Transcription elongation factor SPT5

Histone H3.3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

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