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SMTL ID : 7nkx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1:	5 residues within 4Å: Chain A: C.107, C.110, C.148, G.166, C.167 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167, A:C.167
ZN.2:	5 residues within 4Å: Chain A: C.67, T.69, 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.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:	4 residues within 4Å: Chain C: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95
ZN.6:	5 residues within 4Å: Chain G: C.7, C.10, C.29, T.31, C.32 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.32
ZN.7:	6 residues within 4Å: Chain G: C.75, K.77, C.78, C.103, S.105, C.106 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106
ZN.8:	4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46
ZN.9:	5 residues within 4Å: Chain J: C.31, C.34, C.48, C.51, H.53 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

4 residues within 4Å:

Chain A: D.481, D.483, D.485
Chain V: U.69

3 PLIP interactions:

3 interactions with chain A

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

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.10:

15 residues within 4Å:

Chain U: E.375, R.377, Q.380, G.404, L.405, G.406, K.407, T.408, W.447, D.513, G.777, N.779, R.807, I.808
Ligands: BEF.11

14 PLIP interactions:

14 interactions with chain U

Hydrogen bonds: U:E.375, U:Q.380, U:G.404, U:L.405, U:G.406, U:K.407, U:T.408, U:G.777, U:G.777, U:N.779, U:R.804
Salt bridges: U:K.407, U:R.807, U:R.807

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.11:

11 residues within 4Å:

Chain U: M.403, G.404, K.407, E.514, L.776, G.777, I.778, Q.800, R.804, R.807
Ligands: ADP.10

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Farnung, L. et al., Structural basis of nucleosome transcription mediated by Chd1 and FACT. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-08-25

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerases I, II, and III subunit RPABC1: D
DNA-directed RNA polymerases I, II, and III subunit RPABC2: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerase II subunit RPB11: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: J
Histone H3.2: KO
Histone H4: LP
Histone H2A type 1: MQ
Histone H2B 1.1: NR
Chromo domain-containing protein 1: U
Chromatin elongation factor SPT4: W
Transcription elongation factor SPT5: X
DNA-directed RNA polymerase II subunit RPB4: Y
DNA-directed RNA polymerase II subunit RPB7: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
L

K
a

O
e

L
b

P
f

M
c

Q
g

N
d

R
h

U
W

W
Y

X
Z

Y
D

Z
G

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

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

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

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

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Chromo domain-containing protein 1

Chromatin elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerase II subunit RPB7

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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