SMTL ID : 6ted.1

Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1

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-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.71, C.74, C.81, P.82, H.84 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.71, A:C.74, A:H.84 ZN.2: 4 residues within 4Å: Chain A: C.111, N.152, G.183, R.186 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.152 ZN.4: 4 residues within 4Å: Chain B: C.1196, C.1199, C.1214, C.1217 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1196, B:C.1199, B:C.1214 ZN.5: 4 residues within 4Å: Chain C: C.88, C.90, C.94, C.97 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.97 ZN.6: 4 residues within 4Å: Chain I: C.17, C.20, C.39, C.42 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39 ZN.7: 4 residues within 4Å: Chain I: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.7, J:C.44, J:C.45 ZN.9: 4 residues within 4Å: Chain L: R.35, C.36, G.40, Y.41 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:C.36 ZN.10: 4 residues within 4Å: Chain W: C.20, L.22, C.23, C.37 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:C.23

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain O: U.46 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vos, S.M. et al., Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-22

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
RNA polymerase II subunit C: C
RNA polymerase II subunit D: D
RNA polymerase II subunit E: E
RNA polymerase II subunit F: F
RNA polymerase II subunit G: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
Uncharacterized protein: J
Uncharacterized protein: K
Uncharacterized protein: L
Transcription elongation factor SPT6: M
RNA polymerase-associated protein CTR9 homolog: P
RNA polymerase-associated protein RTF1 homolog: Q
RNA polymerase-associated protein LEO1: S
RNA polymerase II-associated factor 1 homolog: T
WD repeat-containing protein 61: U
Parafibromin: V
Transcription elongation factor SPT4: W
Transcription elongation factor SPT5: X

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

P
Q

Q
R

S
U

T
V

U
W

V
X

W
Y

X
Z

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

RNA polymerase II subunit C

RNA polymerase II subunit D

RNA polymerase II subunit E

RNA polymerase II subunit F

RNA polymerase II subunit G

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

DNA-directed RNA polymerase II subunit RPB9

Uncharacterized protein

Uncharacterized protein

Uncharacterized protein

Transcription elongation factor SPT6

RNA polymerase-associated protein CTR9 homolog

RNA polymerase-associated protein RTF1 homolog

RNA polymerase-associated protein LEO1

RNA polymerase II-associated factor 1 homolog

WD repeat-containing protein 61

Parafibromin

Transcription elongation factor SPT4

Transcription elongation factor SPT5

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