SMTL ID : 7xsz.1

RNA polymerase II elongation complex transcribing a nucleosome (EC115)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.168 ZN.4: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.5: 5 residues within 4Å: Chain C: C.85, C.87, C.91, C.94 Chain R: K.767 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.85, C:C.87, C:C.91, C:C.94 ZN.6: 5 residues within 4Å: Chain I: C.78, S.80, C.103, N.105, C.106 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.78, I:C.103 ZN.7: 5 residues within 4Å: Chain I: C.10, N.12, C.29, N.31, C.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.10, I:C.29, I:C.32 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.9: 4 residues within 4Å: Chain L: C.33, C.36, C.50, C.53 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.33, L:C.36, L:C.50, L:C.53 ZN.10: 4 residues within 4Å: Chain M: C.28, C.31, C.52, C.55 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.28, M:C.31, M:C.52, M:C.55 ZN.11: 4 residues within 4Å: Chain Q: C.6, C.9, C.23, C.26 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.6, Q:C.9, Q:C.23, Q:C.26

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.482, D.484, D.486 Chain O: C.18, C.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.482, A:D.484, A:D.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ehara, H. et al., Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science (2022)

Release Date

2022-09-07

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
RNA polymerase II third largest subunit B44, part of central core: C
RNA polymerase II subunit B32: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: E
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III: F
RNA polymerase II subunit: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase subunit: I
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III: J
RNA polymerase II subunit B12.5: K
RNA polymerase subunit ABC10-alpha: L
Transcription elongation factor 1 homolog: M
Transcription elongation factor SPT4: Q
Transcription elongation factor SPT5: R
Transcription elongation factor Spt6: S
Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II: T
Component of the Paf1p complex: U
RNAPII-associated chromatin remodeling Paf1 complex subunit: V
Leo1: W
RNAP II-associated protein: X
Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p: Y
Histone H3.3: Z3
Histone H4: 04
Histone H2A type 1-B/E: 15
Histone H2B type 1-J: 26

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

Q
V

R
W

S
m

T
n

U
q

V
r

W
u

X
v

Y
x

Z
a

3
e

0
b

4
f

1
c

5
g

2
d

6
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

DNA-directed RNA polymerases I, II, and III subunit RPABC1

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

Transcription elongation factor Spt6

Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II

Component of the Paf1p complex

RNAPII-associated chromatin remodeling Paf1 complex subunit

Leo1

RNAP II-associated protein

Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p

Histone H3.3

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

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