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SMTL ID : 6i84.1

Structure of transcribing RNA polymerase II-nucleosome complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1:	5 residues within 4Å: Chain K: C.107, C.110, C.148, G.166, C.167 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.107, K:C.110, K:C.167
ZN.2:	5 residues within 4Å: Chain K: C.67, Q.68, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.67, K:C.70, K:C.77, K:H.80
ZN.4:	2 residues within 4Å: Chain L: C.1166, C.1185 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.1166, L:C.1185
ZN.5:	5 residues within 4Å: Chain M: C.116, C.118, H.121, C.122, C.125 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.118, M:C.122, M:C.125
ZN.6:	4 residues within 4Å: Chain S: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.7, S:C.10, S:C.29, S:C.32
ZN.7:	4 residues within 4Å: Chain S: C.75, K.77, C.78, H.108 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:C.75, S:C.78
ZN.8:	6 residues within 4Å: Chain T: C.7, F.8, S.9, C.10, G.11, C.46 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.7, T:C.7, T:C.10, T:C.46
ZN.9:	5 residues within 4Å: Chain V: C.31, A.32, E.33, C.34, C.51 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:C.31, V:E.33

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

4 residues within 4Å:

Chain K: D.481, D.483, D.485
Chain W: A.10

3 PLIP interactions:

3 interactions with chain K

Metal complexes: K:D.483, K:D.485, K:D.485

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Farnung, L. et al., Structure of transcribing RNA polymerase II-nucleosome complex. Nat Commun (2018)

Release Date

2019-01-02

Peptides

Histone H3.2: AH
Histone H2A type 1: BC
Histone H4: FI
Histone H2B 1.1: GJ
DNA-directed RNA polymerase II subunit RPB1: K
DNA-directed RNA polymerase II subunit RPB2: L
DNA-directed RNA polymerase II subunit RPB3: M
DNA-directed RNA polymerase II subunit RPB4: N
DNA-directed RNA polymerases I, II, and III subunit RPABC1: O
DNA-directed RNA polymerases I, II, and III subunit RPABC2: P
DNA-directed RNA polymerase II subunit RPB7: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC3: R
DNA-directed RNA polymerase II subunit RPB9: S
DNA-directed RNA polymerases I, II, and III subunit RPABC5: T
DNA-directed RNA polymerase II subunit RPB11: U
DNA-directed RNA polymerases I, II, and III subunit RPABC4: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

H
S

B
Q

C
V

F
O

I
U

G
R

J
W

K
A

L
B

M
C

N
D

O
E

P
F

Q
G

R
H

S
I

T
J

U
K

V
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.2

Histone H2A type 1

Histone H4

Histone H2B 1.1

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

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

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase II subunit RPB7

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

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases I, II, and III subunit RPABC4

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