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SMTL ID : 7nky.1

RNA Polymerase II-Spt4/5-nucleosome-FACT structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1:	4 residues within 4Å: Chain D: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.107, D:C.110, D:C.148, D:C.167
ZN.2:	5 residues within 4Å: Chain D: C.67, T.69, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.67, D:C.70, D:C.77, D:H.80
ZN.4:	4 residues within 4Å: Chain E: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1163, E:C.1166, E:C.1182, E:C.1185
ZN.5:	7 residues within 4Å: Chain F: S.83, C.86, C.88, C.92, C.95 Chain O: R.808, K.813 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.86, F:C.88, F:C.95
ZN.6:	5 residues within 4Å: Chain J: C.7, C.10, C.29, T.31, C.32 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.29, J:T.31, J:C.32
ZN.7:	5 residues within 4Å: Chain J: C.75, C.78, C.103, S.105, C.106 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.103, J:C.106
ZN.8:	4 residues within 4Å: Chain K: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.45, K:C.46
ZN.9:	5 residues within 4Å: Chain M: C.31, C.34, S.36, C.48, C.51 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.31, M:C.48, M:C.51
ZN.10:	5 residues within 4Å: Chain N: C.7, C.10, C.24, C.27, F.31 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.7, N:C.10, N:C.24, N:C.27

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

4 residues within 4Å:

Chain A: G.16
Chain D: D.481, D.483, D.485

4 PLIP interactions:

4 interactions with chain D

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

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

2021-07-07

Peptides

DNA-directed RNA polymerase II subunit RPB1: D
DNA-directed RNA polymerase II subunit RPB2: E
DNA-directed RNA polymerase II subunit RPB3: F
DNA-directed RNA polymerases I, II, and III subunit RPABC1: G
DNA-directed RNA polymerases I, II, and III subunit RPABC2: H
DNA-directed RNA polymerases I, II, and III subunit RPABC3: I
DNA-directed RNA polymerase II subunit RPB9: J
DNA-directed RNA polymerases I, II, and III subunit RPABC5: K
DNA-directed RNA polymerase II subunit RPB11: L
DNA-directed RNA polymerases I, II, and III subunit RPABC4: M
Chromatin elongation factor SPT4: N
Transcription elongation factor SPT5: O
DNA-directed RNA polymerase II subunit RPB4: P
DNA-directed RNA polymerase II subunit RPB7: Q
FACT complex subunit POB3: R
FACT complex subunit SPT16: S
Histone H3.2: TX
Histone H4: UY
Histone H2A type 1: VZ
Histone H2B 1.1: W0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
E

H
F

I
H

J
I

K
J

L
K

M
L

N
Y

O
Z

P
D

Q
G

R
O

S
Q

T
a

X
e

U
b

Y
f

V
c

Z
g

W
d

0
h

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

Chromatin elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerase II subunit RPB7

FACT complex subunit POB3

FACT complex subunit SPT16

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

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1y77.1 | 2aro.1 | 2b63.1 | 2b8k.1 | 2cv5.1 | 2e2h.1 | 2e2i.1 | 2e2j.1 | 2f8n.1 | 2ja5.1 | 2ja6.1 | 2ja7.1 | 2ja7.2 | 2ja8.1 | 2nvq.1 | 2nvt.1 | 2nvx.1 | 2nvy.1 | 2nvy.2 | 2nvz.1 | 2r7z.1 | 2r92.1 | 2r93.1 | 2vum.1 | 2yu9.1 | 3cqz.1 | 3fki.1 | 3gtg.1 | 3gtj.1 | 3gtk.1 | 3gtl.1 | 3gtm.1 | 3gto.1 | 3gtp.1 | 3gtq.1 | 3h3v.1 | 3hou.1 | 3hou.2 | 3hov.1 | 3how.1 | 3hox.1 | 3hoy.1 | 3hoz.1 | 3i4m.1 | 3i4n.1 | 3j0k.1 | 3j1n.1 | 3k1f.1 | 3k7a.1 | 3lel.1 | 3lel.2 | 3m3y.1 | 3m4o.1 | 3nqu.1 | 3po2.1 | 3po3.1 | 3qt1.1 | 3r45.1 | 3rzd.1 | 3rzo.1 | 3s14.1 | 3s15.1 | 3s16.1 | 3s17.1 | 3s1m.1 | 3s1n.1 | 3s1q.1 | 3s1r.1 | 3s2d.1 | 3s2h.1 | 4a3b.1 | 4a3c.1 | 4a3d.1 | 4a3e.1 | 4a3f.1 | 4a3g.1 | 4a3i.1 | 4a3j.1 | 4a3k.1 | 4a3l.1 | 4a3m.1 | 4a93.1 | 4bbr.1 | 4bbs.1 | 4bxx.1 | 4bxz.1 | 4by1.1 | 4by7.1 | 4c2m.1 | 4c2m.2 | 4c3h.1 | 4c3i.1 | 4c3j.1 | 4hga.1 | 4kgc.1 | 4ld9.1 | 4v1m.1 | 4v1n.1 | 4v1o.1 | 4x67.1 | 4x6a.1 | 4y52.1 | 4y7n.1 | 4ym7.1 | 4ym7.2 | 4ym7.3 | 4ym7.4 | 4ym7.5 | 4ym7.6 | 4z2m.1 | 4zux.1 | 4zux.2 | 5c3e.1 | 5c3i.1 | 5c3i.2 | 5c3i.3 | 5c3i.4 | 5c3i.5 | 5c3i.6 | 5c44.1 | 5c4a.1 | 5c4j.1 | 5c4x.1 | 5e5a.1 | 5fj8.1 | 5fj9.1 | 5fja.1 | 5fmf.1 | 5fyw.1 | 5fz5.1 | 5g5l.1 | 5ip7.1 | 5ip9.1 | 5kgf.1 | 5lmx.1 | 5m3f.1 | 5m3m.1 | 5m5w.1 | 5m5x.1 | 5m5y.1 | 5m64.1 | 5n5y.1 | 5n5z.1 | 5n60.1 | 5n61.1 | 5o9g.1 | 5oa1.1 | 5omx.1 | 5ong.1 | 5onw.1 | 5oqj.1 | 5oqm.1 | 5ot2.1 | 5oxv.1 | 5oy7.1 | 5sva.1 | 5u5q.1 | 5vvr.1 | 5vvs.1 | 5w4u.1 | 5w51.1 | 5w5y.1 | 5w64.1 | 5w65.1 | 5w66.1 | 5x0x.1 | 5xf3.1 | 5xf4.1 | 5xf5.1 | 6blo.1 | 6blp.1 | 6bm2.1 | 6bm4.1 | 6bqf.1 | 6buz.1 | 6cnb.1 | 6cnc.1 | 6cnd.1 | 6cnf.1 | 6e0c.1 | 6e0p.1 | 6eu0.1 | 6eu1.1 | 6eu2.1 | 6eu3.1 | 6f40.1 | 6f41.1 | 6f42.1 | 6f44.1 | 6ftx.1 | 6g0l.1 | 6gyk.1 | 6gyl.1 | 6gym.1 | 6h67.1 | 6h68.1 | 6hko.1 | 6hlq.1 | 6hlr.1 | 6hls.1 | 6hts.1 | 6i84.1 | 6j99.1 | 6kw3.1 | 6kw4.1 | 6kw5.1 | 6l9z.1 | 6la2.1 | 6la8.1 | 6la9.1 | 6lab.1 | 6ler.1 | 6ler.2 | 6ltj.1 | 6m3v.1 | 6m44.1 | 6m4d.1 | 6m4g.1 | 6m4h.1 | 6n1z.1 | 6n1z.2 | 6ne3.1 | 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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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